how much of your life are you willing to part with due to daily commute to/from work? you'll need to weigh out time vs money, in large part. many people commute upwards of 100 miles in/out the city daily based on this (and other things like school districts for their kids, etc).
i lived in the twin peaks area for a short time and loved it. after 2 months of searching i found a sizable apartment with 2 parking spots and a great view for roughly 2/3's the going rate at the time (was quite awhile ago so won't bother with numbers now) because it was a unit that hadn't been updated with new carpet/renovated kitchen like most of the other units in the complex. point here is if you have time to hunt/search, you can find some really good 'deals'.
living in twin peaks meant doing your grocery shopping in noe valley or the castro and both "nice areas" of town have the higher rent to prove it. it's also central, timewise, to the golden gate and bay bridges, giving options when traffic in/out is horrible. and, it's a pretty direct route to downtown/financial and places like haight ashbury.
otherwise, there are so many areas of SF that i'd live in today if it was practical so it would come down to what you could afford and what
FLAVOR you want to surround yourself with. every district can have it's nice spots. the one thing i remember most when roving through the city was that you can have a multi-million dollar home on one corner, and they'd be selling crack at the other end of the block, with invisible lines in between/throughout
beyond sf, you'd be facing the aforementioned commute. re bart areas, specifically:
i would avoid oakland (starting at macarthur) through san leandro/bayfair altogether (tho i can't recall the lake merrit stop area and parts of the lake merrit area are pretty nice) but castro valley and dublin/pleasanton are nice enough.
the other direction, berkeley is right near the UC and north berkeley is nice enough, too. i live near el cerrito (equi-distant from both EC bart stops) and it's nice enough but don't bother looking near the richmond stop.
on the yellow line... rockridge to north concord are nice (lafayette and orinda are very nice). through SF, it's gonna be based on how "gritty" of a big city experience you're up for. embarcadero to civic center is definitely downtown and what you'd expect. the mission get's "gritty"
daily city > sfo, i know nothing about. south sf can get pretty rough, tho.
on the freemont line, i've never heard much good or bad about those areas as you move toward the south bay...
it's hard to suggest a particular place without knowing what you're looking for, really. it's all good to someone like me so it's about how much i'm willing to spend (i bought my house in the east bay back in 98 and very much settled, now, so...).
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