By unplugged you mean non electric, or that MTV unplugged thing. The best non-electronic song has to be Bron-Y-Aur Stomp, that song is too awesome. The best MTV unplugged MTV song-thing would be All Apologies.
It's just one of those things i guess. Every time i listen to the song and hear him say that, i really have to wonder how many people in the crowd were like me and just completely subconciously glazed over that little tidbit.
I've got this one mp3 of an acoustic version of "Black" by Pearl Jam. It's way better than the studio version but I have no idea where and when it was recorded.
I'd have to go with 'The Man Who Sold The World' or 'Where Did You Sleep Last Night'. It's a tough call... though I'd probably give the nod to the latter. The screaming chorus at the end still gives me chills.