The curse of the north bay is the lack of trains. BART runs to the east bay, but not the north.
The ferry is basically worthless if you don't actually live in San Rafael. It's a nice ride, but very slow, and not cheap.
Personally, I quite like the bus system: if you don't mind taking the bus, Golden Gate Transit is great. The commute from somewhere like Novato is still long (1hr) but you can use the time to sleep or listen to audio books. Be sure to check the schedules of the express routes you care about: they end kind of early (~6, 7pm) and the non-express routes that run longer take easily twice as long.
Driving is a different story. There are three things to consider: 1) leave early, like 5ish, especially if you're north of marin 2) if you work in the financial district, the time to drive from the edge of SF to parking is substantial and 3) you can park in the financial district itself, but this will cost you around $25/day.
I suppose there's a fourth thing to consider re: driving which is that your drive home is almost guaranteed to be painful if you have to go beyond San Rafael and are not car pooling.
