I think I'm out of my league here.
But too late now, so...
Marv has to be the ultimate, baddest motherfukker, and should def take the overall. Not only is he ugly and big and crazy, he likes women besides. Harvey was prob a bad choice, but figured his character's innards are so pickled from all the substance abuse he's indestructible. Plus, has no morals whatsoever, which must count for something when facing a foe.
I totally think the Tom Stall character outranks Tony, since as you say he can kill with his bare hands while Tony was just a dumb hothead with incest issues. Not to mention Tony dies, while Tom gets all the bad guys and goes home afterward. Plus, he turned a rape scene into a very hot sex on the stairs scene, so once again, he's a killer who kills in bed too.
1. Dalton vs the Keyser: have no clue
but am going with Soze since supposedly he killed his own family without blinking. That's pretty bad.
2. Marv vs Jack Brauer: Teh Marv!!!!!!
3. Scarface vs Tom Stall: Going with Tom Stall as per above
4. Nico vs Sho Nuff: Sho Nuff because I just plain don't like Steven Seagal
5. Bad Lieutenant vs Good Lieutenant: Going to vote against myself and pick the Good Lieutenant
6. Dominic vs Tommy: Dominic because he really was bad. Tommy is too short and also just a hothead. No exceptional skills.