San Francisco - centre of town (almost)
OK, so it's not exactly a rock bottom 'budget' option, but if you're on a bike and want to stay in the centre of the city and do a bit of sightseeing, I can certainly recommend the Motel6 on the corner of Geary and Larkin - It is one of the few city centre hotels that has it's own carpark (underground) and it's only a short walk (3 blocks) from Union Square and Chinatown etc.
I booked on line and got a spacious double room for $80 (that's £40!) a night, and that was over a long weekend - I thought that was great value for the centre of SF?
Infact I was so impressed, I stopped there again on my way back south a few weeks later!
PS. There is a great coffee shop/internet cafe a couple of doors down towards Union Square, and a funky little motorcycle shop right opposite! x
PPS. Motel6 are a great chain of motels if you need a clean/comfy/warm room with space for hanging your washing etc (infact some have laundry rooms on site)... I used quite a few in the US, and they were typically around $40 a night (cheaper than a B&B in the UK!) unless it's in the centre of a major city like SF...