Okay, this is kind of hard since I have so many episodes I have loved and considered my favorites over the seasons, many of which are very good in their own right. However, I do have a chosen selection of episodes that I will immediately say are my favorite if you ask me to answer on the spot. All, I admit, are incredibly biased based on what they contain, which they are:
4.16 "On The Head Of A Pin"
I kind of fallen head over heels with this episode because it was just so good. It was completely different setup since it focused less on the Winchesters and more on the angels. In fact it was incredibly Castiel-centric and focused more on his POV throughout the episode and what he was going through, figuring things out and thinking for himself and understanding that he needs to start making his own choices based on his own sense of morality despite what Heaven may be asking of him, which adds an entirely new perspective of the angelical arc altogether. From the horrific deeds that was placed upon Dean by the angels to torture Alastair to Castiel finding out that Uriel has been manipulating and converting others into wanting Lucifer to rise and destroy the humans, it really was a fantastically structured and written episode and I wish the show would do another episode like this again.
4.20 "The Rapture"
Such a beautifully heartbreaking episode, I just can't not have this in my favorites. Just from the story itself of telling the background of Castiel's vessel alone is something entirely unique and has never been done before to really explore at length the lives of those who are possessed. This is also where we get to see just how amazingly versatile Misha Collins is by shifting back and forth between Castiel to Jimmy Novak rather effortlessly through his performance and showering sympathy for Jimmy even though we all wanted Castiel back. In just one episode. So amazing.
5.04 "The End"
How could I forget to add in this fabulous episode? Perhaps one of the best concepts of having a post-apocalyptic future be shown to Dean, where he meets his future self and sees the outcome if they don't avert the apocalypse and seeing a bleak non-future for humanity. There's future!Dean being cold and distant after everything, future!Castiel that is practically human and turned into a hedonistic stoned hippie where he has no faith and no hope, thus making him a devastated version of himself that makes us sad to see (and thankfully will never see), and of course Samifer. And really now, that ending with Dean and Castiel back in the present sharing that heartfelt moment? LOVE. ♥ So much love for this episode in general, it was very well done and I was impressed with how much they were able to do with this. Dark, bleak, depressing, but hopeful when Dean calls Sam back after being separated to get things back on track in making their own destiny and future.
(edited to add this episode in because I foolishly forgot it the first time around! *facepalm*)
5.18 "Point Of No Return"
There are several reasons why I consider this to be a favorite episode: the writing. The writing was pretty much flawless as far as I'm concerned, from the interactions between characters to the confrontations and what was happening seasonal arc-wise (even if it took away Dean's vital storyline, at the time I thought something big was gonna happen so I can overlook it here), the truckload of fanservice upon fanservice and done correctly without breaking characterization. Most of all, Castiel being a badass resourceful motherfucker while finally giving what Dean deserves, which is a verbal and physical smackdown of the lack of appreciation of all Castiel had risked for him and only to be disrespected by having Dean think it was okay to just give up after everything. I mean wall!slamming you guys. That shit was epic and innuendos galore, like whoa. Seriously, I just can't help but love this episode from all that combined. It's one of my top favorites of season five, much thanks to Jeremy Carver and his awesomeness. ;)
6.03 "The Third Man"
In spite of the sixth season being a clusterfuck of nonsense, I found "The Third Man" to be the rare gems of the season so far. It had Castiel returning, the revelation of whatever he's dealing with in Heaven that is causing a civil war which this episode gives a nice setup for what we have yet to really dive into, Dean and Castiel's ~profound bond~ and their awesome interactive scenes in general, plus the introduction of a new angel character that I have grown fond of, Balthazar. Bonus points for this episode being written by Ben Edlund. :)
Honorable mentions: "Changing Channels" because of the Gabriel reveal, which happens to be the best retcon the show has ever done; I have a soft spot in my heart for "Home" in the first season because that was such a lovely episode, not to mention the S2 premiere "In My Time Of Dying" was perhaps the best opener that continued from a cliffhanger of a finale, jsyk. ♥ Major love for that alone. "Lazarus Rising" and "Lucifer Rising" respectively since they were amazing bookends to the fourth season, kind of a completion of sorts. I also have a love for "Crossroad Blues", since it dealt with the crossroads dealing that becomes a huge thing later on and also dealing with legends like Robert Johnson.
Rest of the 30 Days of Supernatural Challenge.