I've tried all sorts of ways of killing them (the PC manual erroneously claims they are "invincible"), but it seems there are only two tried and true ways:
Knock them into a "kill pit" (such as the sarlacc). You can do this with splash damage from explosives or vehicle blasters (aim at the ground next to them).
Run them over with speeders or wheel droids (tanks and walkers don't work, sadly).
Oddly enough one time I was playing as the Clones on Geonosis and was in that room with the Holographic battle computer thingy (from the movie). There were a bunch of Clone Troopers with me and Mace Windu was there too. After we had secured the room, he just fell over and died! I don't know why... though a guy was "walking into him" right before it happened.
I'm guessing that perhaps as our reinforcements were going down, his "spot" was taken up so the computer killed him. Sort of like if you are doing too badly you lose your "bonus hero." I dunno, or could be a random glitch. Maybe the trooper had bad breath and it sapped Mace's will to live. : (
I remember reading in the previews how the Jedi were supposed to be "very tough" but "never die" and "when they take enough damage they will leave the battlefield."
I also sort of assumed the Jedi were in there in a "time based" manner. Rather it seems like they join at the start and hang around until they are killed and then keep respawning until you're completely out of troops and lose.
I also noticed that getting into a vehicle basically means they will ignore you. You can easily outrun them by bunny hopping away, since they will only ever run and swing.