Hunted: So you didn't like Gordon before,now you can really dislike him. Not only does he shoot at Sam, he beats Dean up, sets a trap to blow Sam up, not once but twice, and makes it clear he's got Roadhouse connections as well. I'm sure Alice will have something to say about his choice of wheels, but not being a car person, I can't even tell you what color it is. I do like his weapons rig though,nifty.
Season two is nothing if not intense for significant episodes and as such Hunted joins IMTOD, Bloodlust, Simon Said, Crossroad Blues and Croatoan on the list of significants for the season,and there are more to come.
Hunted gives us another glimpse at the differences of Sam and Dean, similar to the likes of Scarecrow, Salvation and Devil's Trap Sam and Dean have a difference of opinion. Sam's determination to follow his own course of action repeats what we saw in Scarecrow and another middle of the night (or dark of night) exit on Dean, the difference is this time he tacitly agreed to give Dean some more time, after Dean pleaded with him. Well, technically Sam did give Dean more time,he left him behind. 
Before you think I dislike Sam for this, I don't; it just shows the differences between these two and points us to what we've come to see dramatically in season four; Sam will follow his own path and he's the action guy, especially when it comes to trying to understand what's happening to him. Were I in his position I can't say I'd be different, as difficult as what's happening and the not knowing is for Dean it's nothing compared to what it's doing to Sam,Sam is well aware of that as his comments to Ellen indicate.
Sam: "I'm trying to find answers about who I am, and my brother means well but he can't protect me from that." 
Sam always seems to being searching for answers, who he is, what he is, what's he to become,careful, Sam, too much obsession and too little living in the now is bad for your health. It's interesting (to me at least) that for all Dean's supposed low self-esteem, he does know who he is. It was said back in Skin by the shapeshifter ["I know I'm a freak and sooner or later everyone is going to leave me.] And again here there is another echo, "I wasn't meant to do anything, I don't believe in all that destiny crap." Fatalistic perhaps but also self-actualized.
Hunted shows us blatantly the switch of Sam and Dean regarding hunting, Sam's given in fully to being a hunter whereas Dean has a whole different take.
Dean: "Screw the job, screw it, man. I'm sick of the job anyway. We don't get paid, we don't get thanked, only thing we get is bad luck."
Dean doesn't start reverting back to full hunter mode until WIAWSNB when he finally hashes it out with dad at none other than John Winchester's grave,awesome, Dean who wouldn't go to his mother's empty marker in CSPWDT, chooses to go to his father's fake marker in WIAWSNB, cool.
Hunted continues the blurring of black and white lines. Not only is Gordon off the rails as a hunter regarding the supposed evil he hunts, but he's got no problem hunting humans. We saw in Faith how Sam reacted to Dean's plan to "˜stop' Roy Le Grange and jump ahead to Jus In Bello we see Dean's reaction to killing Nancy, both were in an attempt to stop evil but meant killing a human. Gordon has no such filter, once he's determined someone or something is evil, he kills.
This is a struggle that continues throughout this series, what is good, what is bad, when is it right to kill, when is it wrong. Hunted just ups the ante by putting Sam clearly in the line of fire.
Playthings: Yeah, not a great episode on the whole but who doesn't love drunk Sam? Drunk Sam is glaringly honest Sam. Sam lies very well except when he's drunk, when he's drunk, he lets it all out. He's not kind about it either, manipulating Dean to promise to kill him and using John to do it.
Playthings introduces the idea that Sam is trying to redeem himself, after the events of Croatoan and Hunted it's a natural progression and he follows up on it in Houses of the Holy, so I love that the characterization continues to build. It's also an important characterization for Sam in season 4 as well as Dean,so say what you want about this episode an important character development began here.
A little mournful nugget for you that caught me the first time and each time I've seen this episode since (which granted isn't a lot): 
Sherwin: [as he and Dean were discussing the sad times of Rose having to leave the old family home] "Well, would you be [sad] leaving the only home you ever knew?"
Dean: "I don't know; I never really knew one." 
Funniest line: 
Sam: "Dude, you're not going to poke her with a stick."
Nighshifter: Hello, Ronald. A shapeshifter is wreaking havoc, Sam and Dean are Feds, but not the men in black, mandroids are real,sorta, enter Victor Henricksen and Renegade,this is a very satisfying episode. It stands alone or it can be watched along with Folsom Prison Blues and Jus in Bello, and the final bit in Are You There, God; it's me, Dean Winchester.
I see Nighsthifter in two parts; the first part is a bit more carefree, innocent. Ronald the oft-forgotten civil servant becomes research/investigator/hunter after a shapeshifter arrives in town. Ronald's research is top-notch and while he has some awareness of the danger, why else carry a machine gun, he is pretty clueless about the real danger. Once he was gunned down, the feel changes. Enter Henricksen. 
Once Henricksen arrives. it's a whole new level of tension. Who didn't love the rapid fire exchange over the phone between Victor and Dean,if it's been a while, pull out the DVDs and cue it up.
I'll have more on Nightshifter in my article on Ben Edlund scripts"”yes, those of you not fond of Mr. Edlund's writing (and I am so not one of those) he wrote this one. Final thought,Renegade,
Houses of the Holy: An excellent follow up for both brothers. Dean has to lay low due to recent events in Milwaukee and Sam is still desperate to save himself, or have someone save him. At the end Dean promises Sam that he's looking out for him and while Sam affirms that he knows that for the first time he admits that might not be enough.
Again, the idea of when to kill and when not to kill is the underlying theme as well as what is and what is not evil.  Other themes woven here are Sam's belief in a higher power and what we already know is Dean's disbelief. In the end Sam suffers a blow while Dean perhaps sees a glimpse into something bigger.
And of course Kim Manners brings it all together.
Born Under a Bad Sign: Season two has so many powerhouse episodes that it might be easier to list those episodes that aren't significant rather than listing those which are; BUABS joins all the others before it as significant, and like Croatoan, we don't have all the answers here.
So why did Meg possess Sam, was she really trying to kill him using Dean as her hammer? Was she simply tormenting Dean for sending her back to hell? Had Meg given up on playing her part in Azazel's grand scheme or was it something more? Did the demons know that John had told Dean he might have to kill Sam and thus were testing Dean's resolve? There are so many questions that I do not have the answers to but this is an episode that can be watched again and again and I never get tired of it.
Bobby makes a welcome and long overdue return, IMTOD was the last time we saw him. Dean is pushed farther than he has ever been regarding Sam and while we now know he sucks at making deals, he is a hell of a gambler sticking to his hand that Sam couldn't be capable of what the evidence was telling him. Dean may be a soldier, Dean may suck at crossroad demon deals [as in really sucks] but Dean follows his instincts when it comes to family and he is rock solid.
Sam, I cannot imagine what being possessed and seeing some of the things he saw did to him. Did what happen here help propel him to who we saw in season 4 where he was all about control at all times? Surely we know that control is important to Sam so there's no way being possessed was something he simply got over. I agree with those in the fandom who suggest that it was too little and too late to see a follow up on this idea in Jus In Bello, I'd say much of season 4 has made up for it.
Tall Tales: Bobby, you're awesome, and that's before we knew about your panic room! The premise is cool, Bobby arrives and the two brothers explain their predicament. What a riot. Both brothers look like fools, both actors willingly make fools of themselves to deliver, there's pranks galore, Lady in Red, probing again and again and again and again and again and one more time and, of course, one of my favorites,the Trickster. It's worth a watch anytime you're feeling blue, or frankly just anytime.
Roadkill: The first time I saw this one I wasn't that impressed. I thought Sam was maudlin [in the Webster's definition of "˜weakly and effusively sentimental] and Dean cold and overtly detached, in other words, both characters were noticeably out of character. Now, having seen it a few additional times, and having the benefit of season 3 and season 4 to frame my opinion, I'm amazed at just how telling this episode is especially regarding Sam's state of mind and where he will ultimately go.
Heart: Another episode that left me a bit cold the first go around, so much so that I didn't bother with it for quite some. Now, having watched it again I'm impressed with the foresight of Sera Gamble. Much like Raelle Tucker did with Roadkill Heart delivers a much more powerful punch once we've gone forward and seen where both Sam and Dean have gone in their journey. In other words, these episodes hold up over time.
Supernatural gets a rap in the fandom for being to Dean-centered because his storyline appears more in the forefront; I disagree. Season 2 is clearly about both brothers' journey, emotionally and shall I say cosmically [as in the universality of heaven and hell and destiny and free will].   In Heart Sam is confronted again with good versus evil, whether something is truly evil simply because it portrays monstrous tendencies. This is an excellent follow up on Bloodlust as it has Sam confronted again with the very choice he dealt with then, kill Lenore because she is a vampire or let her go because she's chosen a new path. Bloodlust ended happier, Heart is sorrowful; Sera Gamble wrote them both.
Dean similarly continues with his emotional journey that began in some respects back in Bloodlust. Back then he was happy to be going after vampires and anything evil. Here he is almost giddy with excitement at the prospect of hunting and killing a werewolf that is until he kills one and watches it turn back to a confused, frightened and dying man. 
In Bloodlust Gordon saw only evil, Dean did too until who and what Lenore was shifted his paradigm. In Roadkill it was Molly's perceptions that needed to be shifted; here it is both Sam and Dean who get their perceptions shifted. Not everything that appears evil is, not everything you see is reality, not everyone you try to save can be and not everything you kill deserved to die.
Hollywood Babylon:  Inside jokes galore, there's no way I'm neither knowledgeable enough, nor willing to write them all down, to put them in here. Needless to say I laugh at something new each time I watch this one. The one mark against this one, no Impala, otherwise it's a hysterical send up of horror movies with bad acting, bad writing and idiots roaming all over the place.
Gilmore Girls, "˜what's up with this weather, it's nearly Canadian, seeking safety in a ramshackle house that's a set piece thus only three-sided, and sooooo much more make this one enjoyable each time as you go through it and pick out new bits. It's also a bit of an emotional safe zone after the agony of Heart, and prior to WIAWSNB and AHBL I & II. It may not further the mytharc but it gives humor and hunting and food and foolishness (and yes, I'm picking words that start with the same letter) and frankly it's great to watch after popping some corn and settling in for a night of fun, I suggest Tall Tales and Hollywood Babylon as a double feature. Only one was written by Ben Edlund. 
Folsom Prison Blues: Set in a prison this could be almost as much of an anti-climatic disaster as Phantom Traveler in that I knew the plane wouldn't crash but because it keeps moving right along it doesn't fall into that trap. Further this brings us Victor Hendrickson again and he's just as snarky and unimpressed with the Winchesters here as he was back in Nightshifter.
I'll admit that I got caught in the whole "“ oh, so you're Deacon surprise. Even though Deacon had been in several scenes with Dean and Sam I'd never figured out it was him until the reveal. Maybe I should have seen it coming, I don't know, but I enjoyed his reveal,and the fact that Dean laid a nice punch on his jaw at the end. Thank goodness we got a moment or two of the Impala and I have to say that I agree with Dean's sentiment as he broke out of the prison and found her, "A sight for sore eyes." Course now, two seasons later, that phrase has a different meaning but back then it was purely innocent.
What is and What Should Never Be: Alternate realities are really, really risky but Supernatural dares to go and goes well. Dean is getting a chance to make a decision, stay or go. He had that same decision to make in IMTOD but the opportunity was stolen from him by John's deal. Here he confronts it and chooses his course.  I'd say that's significant.
It may not add to the overall mytharc but it adds to the characterization. Dean is deeply affected by his lack of relationship with Sam and based on our knowledge of both characters (and from what we saw in The Pilot with Sam's dreams for the future and Dean telling him to ditch the interview) without hunting, this is very likely what these two brothers would have been like. 
In the end, the hunter in Dean "“ the one Zachariah helped reawaken "“ comes through and he's not fooled by this idyllic illusion. Sam's doggedness in hunting down his missing brother may not have gotten any screen time but the fact that he stole a car (assumed "“ or borrowed *ahem*) and tracked Dean's location to rescue him are all evidenced by his arrival. As for "˜bizarro world Sam' his loyalty shines through as well, even as he is embarrassed by the brother who apparently gambles and looses and steals mom's silver to pay off a bookie, he's aware that all is not as simple as big bro Dean is passing it off to be and in the middle of the night accompanies his brother on whatever lame brain mission he's on.
A very different Sam than we're used to without a relationship with Dean but both the first time Dean calls him and says he doesn't know where he is and then over the silver chest, Sam has concern for Dean. 
Each time I watch this episode I see something different, either something I missed or I evaluate something differently, to me that's the mark of a great episode and no surprise to me, Raelle Tucker wrote this one.
All Hell Breaks Loose I & II:
It's tough for me to break these into two so I'll just go into them together, for they are (I believe) meant to be dealt with as a whole.
I think it's important to note that this series has a tendency to separate the boys when something significant to one of them is happening; it may annoy the fangirl part of me but the truth is that no matter how close we are to someone we are all in these journeys called life on our own, no other human being can truly know what having an illness or a loss or an emotional crack or curse truly feels like. As much as I applaud Eric for going against what was popular and sending Dean back alone during In The Beginning, I applaud him for separating Dean and Sam here in AHBL I. True, Dean spent much of the episode driving from location to location hunting Sam,but this was an episode in which Sam was finding out a lot about his curse, the things that had happened and were happening to him and it had to be that way. 
Sam and YED have awesome, and I do mean AWESOME, moments here. Can you imagine being side by side with something so patently evil, something that as Sam said "˜ruined' your life? Whew,that he walks away (well, in the end not so much walks) still able to speak is incredible. As much as I want to shake Sam to make him tell Dean what YED revealed to him I get why he didn't. How do you tell your brother that the mother he remembers (and you don't) died "˜cause she was in the wrong place at the wrong time, and that she recognized the demon who, by the way, dripped blood into me, your little brother, into my mouth, you know, all before mom burst into flames, you carried me from the house and life changed forever as you knew it.
What is very interesting when Dean does ask what else the YED told him is that Sam lies quite badly,Dean recognizes the lie but doesn't call him on it "“ likely too wrapped up in the whole deal he just made and still trying to figure out how to get around that "˜awkward' subject that will come up in oh, say 365 days,hey, Sammy, did you hear that hound barking????
Sam gets a whole lot better at lying. Just watch all of season four.
Sam here doesn't kill Jake, similar to not killing Gordon in Hunted, he turns away. Sam, you should have paid better attention, sure in Hunted you had the cops on their way but still there were a lot of bullets flying and you could have been hurt or killed, why didn't you learn? Well, he did, as Jake learned at the end. That was cold.
AHBL II sets up basically all of season three, which is also probably why it got a bit out of control so that in the end the whole John, Dean, Sam shot was shot one way and then had to be redone as Sam needed to be dressed differently, not so bloody. Dean makes the deal that bookends John's, YED taunts Dean yet again, only this time Dean gives back much better, demons are released "“ yep, that means Lilith, the clock is ticking for Dean, and Ellen makes her last [?] appearance. I like that the tag at the end has the two brothers hitting the road with work to do, it is a nice holler back to The Pilot and I'll go on record and say that Sam's confronting Dean about the deal is an awesome brother moment. Sure Bobby and Ellen spoil it at the last minute, but that's what the pause button is for. I love it.
I'll also suggest that Eric learned something from that scene, we get awesome brother moments in NRFTW as well as Heaven and Hell that improve greatly on this ending so I'll give him credit, after all he's growing in the craft and doing it right in front of us.

Season two was an awesome season and frankly too big for me to ever capture it in a recap like this but I gamely tried and now after 7,340 words you're still here (eyes crossed and everything).
BTW, just for the heck of (and to torture myself) I'll be doing some article on favorite episodes of each season,stay tuned.
Thanks for reading.