Depends on what you mean about not costing the earth ... you might get some interesting enough deals in these places right now. Must confess as a local I haven't lodged in any of these places, but go by 'facilities' I like to use:
The Clift Hotel since I like the Redwood Room a lot
Hotel Vitale for the waterfront location, again a great bar, will be more expensive than the Clift, probably around 200 quid a night.
The
JDV hotels (of which Vitale is one) are certainly quirky, nor your usual chain hotels, some are in 'interesting locations', shall we say, bordering the Tenderloin or some of the less savory locations in SOMA, but are priced at all points. They give you a good idea of the range of potential prices for not so typical hotels, and where you might need to stay in SF to pay the price you want.
EDIT - you may well have been before, but it's worth pointing out that getting into the central area from Pacific Heights, say, is very quick, and some of the JDV places there can be had for less money. SF itself is a small place.