Craigslist and Padmapper are the best. I just did this, it took me about a month and a half to find a place. I ended up getting a place in Noe Valley of 27th.
I drive the 280 every day now to Palo Alto. After 9:15 am from Noe Valley and after about 6:30 PM, it's a breeze. It takes me 35 minutes total, and I got 75.
If you don't want to drive, Portrero hill is your best bet. If you don't mind driving, Bernal, Noe, Glen Park or the mission (or portrero) is your best bet. Castro, SOMA, or anything north/west will pretty much suck unless you leave after 10am.
The real problem with RWC is that it takes a long time to get to the downtown section from the 280, so you might have to think about the 101, which WILL suck, no matter what. The 101 doesn't really settle down at night til 7 or even 8.
I've only tried a short stint from PA to RWC on it in the mornings and usually that sucks too.
Portrero is your best bet for caltrain though. You'll probably spend $150 a month on caltrain passes. The big thing there though is you'll have to find somewhere in portrero/dogpatch to stay, and I think that's harder to do because there seems to be fewer places. Also, if you live there, you'll probably want to live close to 18th or 3rd to be within walking distance of anything.
Check walkscore.com for any places you find to see what's around them.