"Single Room Occupany" hotels, usually occupied on a weekly or monthly basis. SF regulations has turned them into long-term homeless shelters, in some cases the city even pays the rent for the really low-income residents. Many people living there are on social security/disability checks, veterans checks, or work occasional jobs. Some but not all are drunks/druggies/criminals but enough that no one with the money to stay elsewhere wants to be there.
Union Sq is your best bet for very close to BART/MUNI (look for something closer to the Powell or Montgomery Stations than the Civic Center station) and good neighborhood.

Contrary to what's posted above there are non-flophouses to stay in the Mission. There have been mixed reviews of the Elements Hotel/Hostel, but the bar is always hopping and the location is central, if you like urban.
There are also B&Bs on this side of town, including a bunch in Noe Valley (near the Mission, quieter/fancier). Probably a better investment.
B&Bs in Noe area
Union Square and the area nearby South of Market have big convention hotels, which Priceline and Hotwire discount if there's space. They are clean, potentially safe, and sterile, in an area with little charm but good access to the Disney store.

OP, San Francisco is compact enough so that you shouldn't worry about the location of a Union Square hotel relative to the Mission District. It's a big city, and they have contraptions called taxicabs. They roam the streets, ready to give rides back to Union Square for the price of a couple drinks. By the way #9, the first time I encountered the term SRO was in relation to welfare hotels on the West Side of New York. This thread is the first time I've seen the acronym used to describe flophouses in 'Frisco.

But Willy... It's San Francisco where Newspeak is the official language. Where normal folks are considered second class.

San Francisco has always been full of itself. It's part of the charm, at least for a tourist.

yeah im going to sf too.
my questions are:
1 anyone have an experience or view about the red victorian ? is it real or just fakey fake for the tourists ?
2 do the buses from there up market street run often and late ? ( #s 7 and 73)
3 where's the best bicycle shop ?

Red Victorian Movie house on Haight? Not for tourists. Just indie films and unusual seating. Worth a visit. Red Victorian B&B? Crappy touristy, neo-hippy-ness.
The 71 Haight-Noriega bus runs till a little after midnight both weekends and weeknights (goes along Market to 5th St). The 7 bus is a commuter timed bus, running only morning and evening rush hours. There isn't any 73 bus.
Haight St to Market is walkable, although a little dubious very late at night and there are a few steep hills walking from Market to the park-end of Haight.
Check Yelp.com for local reviews on bicycle shops. Not sure if you mean to buy or to rent or even where in town you'd want it.