Realistically? The most logical answer is Metropolis or Pull Me Under, Spirit, and As I Am. 3 of their biggest songs, all great concert songs, casual and die hard fan favorites. That'd be a killer encore right there, actually.
Songs that I think should be played WAY more than they are? The Glass Prison (how this juggernaut of a song didn't become a live staple baffles me to this day, 14 minutes or not.), The Dance of Eternity (yeah they just played it last tour and a little bit in 2010, but this song IS Dream Theater to me, so I feel like it should be a live staple. Entertaining as hell to watch them master it.), either LFaGA or TOTHtStS, as they're awesome and WDaDU is criminally neglected live.