I think contenders for best episode, (And I can only narrow it down to a couple a season) tend to be ones that I can watch again and again are:
Bewitched , Bothered And Bewildered. Passion: I can't really separate this couple in S2, comedy gold, and real tragedy.
The Wish: Everyone gets to play a different version of themselves and do it brilliantly. VampWillow gets a lot of the attention but SlayerBuffy and desperate Giles are the favourites of mine here.
Plus Doppelgangerland- a Willow centric episode and the sequel.
Hush: Can't really add anything to what's been said.
Who Are You:Bodyswap, Faith-centric ep. SMG and ED are great at playing each other. Plus its actually really funny. ('Bondage fun!' What's a stevadore?' and so forth.)
The Body: One of the few truly accurate depictions of grief I've seen on a television show. 🙁
The Gift: Also incredibly moving...
Life Serial/Tabula Rasa: I like the comedy episodes in S6, and their few and far between, but these are good. I also consider the final three to be quite strong.
Conversations With Dead People: Creepy, shocking ep that stays with you.
End Of Days/Chosen: Not perfect, but it has so many great scenes with the characters I love. Xander/Dawn, Buffy/Faith, Angel comes back, Caleb gets killed (hate that guy!), Buffy cheers the hel up and becomes recognisable again.
Out of all those...I'd take Hush/Who Are You to be the best of the series- can't pick between them. 🙂