I'm a cover junkie, and I have to say that (besides the covers that have made it onto the albums, such as Me and the Bean or Don't You Evah, which are Spoon songs for all intents and purposes) my favorite is probably Britt's version of John Lennon's "Isolation." HOWEVER, they've been doing a live cover of the Stones' "Rocks Off" lately that is pretty killer. I've been looking for a bootleg of it for months now; if anybody has one I would be forever indebted if you would share. A partial recording on YouTube is the best I've been able to do.
On a related note, at the Nashville show last October this "setlist" was passed out. It shows a lot of cover songs they didn't play (they did do "Lowdown" as the last song in the encore) but I'm wondering if any of you have seen them do any of the others (listed in the caption) live? It would be cool but weird if the band actually knows all those songs but never plays them.