You know the drill. Who wins?
Snake Eyes, easily. Jack Bauer and Chuck Norris together wouldn’t stand a chance against him.
Ding Chavez.
Snake Eyes is a ninja. Jack Bauer is neither a ninja nor a pirate. He doesn’t stand a chance.
You must remember that Jack Bauer is the anti-Batman. He’ll lose if he’s prepared, but he’ll always win if he’s caught flatfooted or winging it. Since ninja tend to use ambush tactics, that plays into Bauer’s hands.
I daresay that Jack Bauer would win in a karaoke contest.
Snake Eyes. Even before he was an overblown, overexposed super ninja, he had the most dangerous foot in the US Military.
Look at his filecard, 12 different unarmed fighting systems, edged weapons, mountaineering, arctic, and desert survival. What does Bauer have? the ability to yell that he has less than 24 hours to do something?
I’m going to go with Jack. He’s deadly with a pistol which nullifies a lot of those unarmed fighting systems. And you can tie him to a chair and beat him half to death and he’ll still rip out your throat with his teeth and then put in a full day at the office hunting bad guys.
Nicolas Cage. It’s fight night!
Can we all at least agree that, were they teamed up, Snake Eyes would definitely be coming home in a body bag?
-Joe
Snake Eyes. The hero always defeats the villain.
I’ll see your pistol and raise you all NATO and Warsaw Pact small arms. Plus the dude’s got a pet wolf. A pet frickin’ wolf! What does bauer have? An annoying daughter who gets trapped by mountain lions and hillbillies with bomb shelters.
Well, Jack also has a hacker so skilled she could probably use a computer to make Snake Eyes’s sword jam. Plus an infinite supply of bullet-catching nonamers.
-Joe
Snake Eyes beat Firefly and his unstopable Scorpion Formation. You can’t top that shizitinit.
One thing for sure, Jack’ll never make him talk.
I lol’d 
Of course, if the Snake Eyes came from the cartoon continuity, Jack might come out on top. Did that version ever do anything notable other than dress up like Boy George and dance around with Shipwreck? They even gave his rivalry with Storm Shadow to freakin Spirit.
But he has come back from the dead a couple times. Could he possibly get some Zombie mojo from that?
Well, traditionally zombies haven’t been able to do much against ninjas, so it wouldn’t help him all that much.
Someone mentioned Jack’s computer genius sidekick, which makes me think that Jack might actually have a shot. As everyone knows, pirates are ninjas’ most formidable foes. What she could do is re-route all the Internets (all of them!) to Bit Torrent, which would significantly reduce Snake Eyes’ power level and give Jack a fighting chance.