This is not a simple question and I will not be drawn into a simple answer. As with many things, it depends on the situation.
- One-on-one hand to hand. Both characters are experts in hand to hand combat. I have seen both of them knock out highly trained mercenaries and military personell with one well-placed attack. However, in this fight, I give the edge to Jack. Sam's attacks rely on stealth and surprise. Jack, on the other hand, can kick your ass face to face. For this reason, I give it to Jack. It's a tough fight, but the end is never really in question.
- One-on-one with weapons. Sam has the far greater arsenal. In this situation, his stealth capabilities and advanced tech take Jack out before he even gets close to Sam. Smoke grenades, sticky shockers, night vision, etc. Not to mention a kick-ass sniper rifle. This is like Sam being told to assasinate a terrorist, but the terrorist has no guards, no security, and no chance. Sam is a one-man killing machine. Jack shoots randomly into the shadows, but Sam puts him down in under 30 seconds.
- The ultimate test. In this senario, Jack has all the resources of CTU at his disposal and his mission is to find a spy (Sam) who has infiltrated CTU. Sam's mission is to sneak into CTU and assasinate their top agent (Jack). This is the fight I dream of. Jack knows Sam is coming, and CTU is on alert. Sam has access to all kinds of intel on CTU's security and defensive capabilities. However, he is also restricted from killing any CTU personell other than Bauer. Sam's equipment and stealth abilities will be put to the ultimate test. Jack's leadership and the CTU staff will shine. It would be awesome. All of that being said, we have seen that CTU's security is not fool-proof. Little by little Sam moves through the shadows (why is it so dark in there anyway?). Jack may know he's coming, but he certainly doesn't know when or where. Security cameras start malfunctioning for no apparent reason then appear to be fine moments later. Guards just start vanishing. Jack is nervous. He puts CTU on high alert, sure that Sam is in the building. BANG! Lights go out. Chloe finds Edgar in a blubbering mess on the floor and proceeds to bitch him out for not widening the search filters on the CTU computerized security system. The next instant, she finds herself in an inescapable choke-hold with a mysteriously familiar voice whispering in her ear. After Sam forces her to disable all of CTU's automated security, he uses her as a human shield and moves confidently through the dark. Jack, meanwhile, has called former president Palmer who drops the biggest bombshell of the season: he leads a double life as the Head of Third Eschelon - he is Sam's boss and he ordered Jack's assasination. Jack's priorities shift from defense to escape. He knows CTU like the back of his hand and makes his way to the garage. This is his mistake. He believes that he is safer trying to escape than he is behind his bulletproof glass in the office. Even in the dark, his highly trained senses hear something moving toward him. He sees three unusually bright green lights floating about six feet off the ground and recognizes them as night-vision goggles. He fires! Hears the distinct sound of a body hitting the floor. An instant later, Jack is dead. Jack actually killed Chloe. Sam already had his pistol aimed at Jack's head when Jack fired. Sam succeeds in killing Jack, but Chloe's death breaks the "no kill" order and the mission is a failure. Everybody comes back to life and Sam has to start over from the beginning because some moron never bothered to save the game.
So there you have it. I'm sure there are other senarios in which Jack Bauer has a better chance, but stealth assasination is Sam's bread and butter. In fact, Sam has handled more difficult assignments than this. Note also, that Jack was virtually flawless. He did everything right. The problem for Jack is that CTU is full of incompetent boobs who aren't worthy to carry his bullet-proof jock! Sam, on the other hand, has only himself to worry about and rely on - and he is always flawless.
For your own information, Dennis Haysbert plays president Palmer on 24 and voices the head of Third Eschelon in Splinter Cell. That's for those of you who didn't get the joke.