I am a sucker for the Layla instrumental by Derek and the Dominos, but that's likely because it brought together a perfect scene in a great movie.
A personal fav that never gets any love is the guitar finale to Soulshine by The Allman Brothers.
http://www.youtube.com/watch?v=G3WuSBo-lIE
This song is full of great guitar work by two of the best of all time. Main guitar solo starts at 4:40, and the 2nd guitar joins at 5:30 where it really takes off.
And Tom Morello has too many good instrumentals to list, but one of his best is from Audioslave's "Doesn't Remind Me":
http://www.youtube.com/watch?v=zOMSB7s15C8
Starts at 2:55.
If you are a Pearl Jam fan, you have to love Mike McCready's guitar solo in Yellow Ledbetter.