Drums/Space are by far the most frequent - being in the hundreds. I imagine "Not Fade Away" is possibly at the top of the list of real songs. That's the song I saw the Dead play the most (26), so add in the bazillion offshoots and cover bands, that's probably up there.
Non-Dead contenders:
Losing My Religion (30+)
When I Go To The Beach (a couple dozen or so times)