Either/Or is great and, it might not be what Elliott would have wanted, but it always makes me think of Good Will Hunting...which is a movie that I absolutely adore. Say Yes, Between the Bars, Angeles, and Ballad of Big Nothing are my faves on the album I think. Also, Miss Misery from the GWH soundtrack is a great song.
But my favorite all-time Elliott Smith song is Twilight. I might have mentioned this before but a good friend of mine's girlfriend is a really talented singer/guitar player and she does a heartbreaking cover of that song. Lovely. Also, the Vampire book series is based on the song, FYI.