Freeman would definitely beat Master Chief. Chief has two weapons at any given time. Freeman has...*Counts* 10 weapons at all times. And with items to use as shields in front of him (And hurl at MC for a definite instant-kill), there's no question as to Freeman's victory. MC is, for a future-FPS character, surprisingly wimpy if we just look at gameplay. (He is much less durable than Freeman, and infinitely less durable than Samus Aran, for example. And that's just a pure "How long do they survive under fire?" thing, don't MAKE me get to weapons and ammo...)
That said, I'd love to see...
Master Chief versus Nathan Hale. Now THAT is a pretty even fight. Hale has two separate weapons that make cover useless, and his assault rifle has a great grenade launcher on it. Master Chief has the recharging shields and the instant-kill sword (if he can get close enough to use it, that is...)
Kratos versus Dante. This is one for the history books. What will win, cocky attitude or blind berserker-rage? (The smart money's on the first, the cocky and funny one always wins, Hollywood taught us that much)