I really wouldn't recommend relying on the Yolobus. In my experience, they're seldom on time and not the most well-maintained buses in the world(plus, full of the types of crazies you'd expect to encounter in a much larger city). The traffic from West Sac to Davis in the mornings is pretty awful, and the people I know who commute(by car) say it generally takes about 40 minutes to go the 12 or so miles, plus extra time finding parking in the overpriced and overfilled parking lots.
The apartment complexes are usually full of undergrads and can get pretty loud on thurs/fri evenings -- daviswiki is good for letting you figure out which complexes are good for avoiding that type of situation though. I lived in apartments for my first two years in Davis -- one was awful (University Square -- poor maintainance, noisy neighbors) and the other was SUPER but you have to get on a waiting list (Davis Townhouse -- super quiet, lowest price in town for a 1br but still pretty steep). I live in a house in East Davis now (moving to north carolina if anyone wants to take my spot!) and I think it's the best option if you don't mind sharing with people. Basically anywhere in Davis is close enough to bike to campus, and if you're not a biker the Unitrans buses are super.