The Moffatt House
Reasonably inexpensive B&B lodging.
Great Highway Inn
A no-frills motel across the street from the beach.
Geary Parkway Motel
This former dive has been completely remodeled with clean rooms, nice televisions, microwaves, blowdryers, irons, and mini fridges. Reasonable prices, safe and neat - the owners have put a lot of effort into making this motel quiet and nice.
Seal Rock Inn
Nestled at the westernmost edge of the city overlooking The Cliff House and The Sutro Baths' ruins, this hotel has a small pool, volleyball court, and restaurant. You're a bit out of the way from downtown about a 30 minute drive/bus, but a great location for someone who enjoys San Francisco's nature, or who will be heading to Marin or down to the peninsula, as you are on the other side of most of the clogged commuting routes.