There are some great old houses in South of Market, but turnover is rare, and they're all expensive. There are some great/awful new live/work buildings there too, but most of them are condos and all of them are expensive.
Affordability comes in Outer Mission, Excelsior, Outer Richmond, Outer Sunset. Occasionally Potrero Hill toward Cesar Chavez. "Affordability" is relative of course, but if you're finding yourself priced out of the places that everyone talks about and look nice on the map, check prices in the places I listed.
Also, remember that East Bay near BART is closer to South of Market than most of San Francisco city is, time-wise.
This is assuming you don't want to live in Bayview.
Studio: $2000-$2700
1BR: $2500-$3200
2BR: $3100-4000Depends what part of the East Bay, of course. West Oakland is the closest BART station, but it is in some serious ghetto. Lake Merritt, Berkeley (esp North Berkeley) and Rockridge are your first good options, but they'll take a little longer to get to. My advice would be definitely to check out Rockridge, it's a surprisingly nice part of town.
Actually the Dogpatch area has come a long way in the last decade or so. Not much of a secret any more, and low turnover, but still relatively cheap, easy access to South of Market (or 101), and nicer than many other options. Low walkability, but easy parking...
And unless you have 3+ months to look for a place every day, don't expect:
1. A bargain 2. That you will get picked for said bargain
Moving into an older, but more sturdy unit is the most sensible thing we have ever decided to do.