Well, we can't really give advice on which college to choose if you don't say what you personally would want out of a college...but in general the Bailey colleges (University/Castle, Johns, Chads, Cuths, Hatfield and sortof Hild Bede though that's far out on it's own) are more traditional, with the main exception of Cuths. The Hill colleges (umm, all the rest, look them up) are newer and generally less traditional, though some are still quite traditional. I'm at Trevelyan personally and I've found it has a nice balance between being "modern" and traditional in that we have gowns and fortnightly formals.
These colleges are generally closer to the science site with the bailey colleges being closer to where the arts/social sciences are generally taught, if location's another consideration. But then again in Durham nowhere's that far away really. Although I haven't done the walk personally I'm guessing even Hild Bede to the science site would still only take around 25 minutes.
Let us know what you want out of a college (size/location/tradition/rooms/catering/whatever else you think of) and we'll be able to give you more of an idea which college you'd be best suited to from the info you give us.