Pathfinder, you chose what your favored class was, and if using the optional variant, gain extra bonuses depending on what that class was, and what your race was. I haven't played it in over 5 years, so can't remember, but I'm pretty sure that at least the default, you got a thing for every so-many levels in the class. Default you got like +2 skill points (or was it +1?) each time you took a level in your favored class. I think there's one where you deal an extra 1/3 damage when doing something from the class (so every 3 levels, you deal an extra +1 damage). Much better than 3e's version, where all half-orcs had a favored class of barbarian, thus shoehorning them into that steretype (same with gnome illusionists/bards, elf wizards, halfling rogues, etc).
As for multiclassing, I tend to disclude it from the games I DM. Though, my players seem to be more story oriented than power oriented, which then I wouldn't have a problem with MCing. The game I play in, I MCed, but it was story reasons. Unfortunately, I am not having fun, as the new players added after previous players left have all been power oriented, making every choice based on the numbers, which makes my MCed character not fun at all (she's not the best at pumping numbers, being a redemption paladin/fiend warlock/barbarian (one level) ). Thinking of retiring her.