This might change after I've watched the whole season over again (which I can't do until I get the DVDs, THANKS A LOT, stupid DVR), but for now, these were my favorite episodes of this season.
"Weekend at Bobby's"
Dean's edge aside, I loved getting insight into Bobby's life. There was so much humor, and pathos, too, because my god, he must be lonely.
"Clap Your Hands if You Believe"
The story-of-the-week was delightful, with evil fairies and alien abduction and "crazy" people who knew what they were talking about. But really, the best part was seeing Sam freed of the constraints of hiding himself from everyone. It was a step beyond knowing why he was acting so strange, and I loved watching him acting at a whole new level.
"Appointment in Samarra"
Death is just an awesome character, and Dean's courage in seeking him was fantastic. It was great to see Tessa again, especially with her attitude toward Dean. She was a little tired of his defiance of the natural order of things.
From episode 15 on, things just got really good. "The French Mistake," because I love the meta. "My Heart Will Go On," because of the way they changed everything. I had to laugh that they were driving a Mustang, because of Kripke planning to have them drive that, and being told by his neighbor that it's a good car for pussies. "Frontierland" and "Mommy Dearest," finding ways to bring back old threads and old guests. Samantha Smith just rocks every time she's on.
"Let it Bleed" killed me, with Dean making that big sacrifice, and I will forever be impressed with Jared Padalecki playing FOUR different versions of Sam in "The Man Who Knew Too Much."
So that's my list of favorites. What's yours?