Inexpensive + Location + Clean.
50's motor inn - It's a bit worn but not in an offensive or malodorous way (sometimes you might see a little peeling paint, or older furniture). The bathroom was small, but my room was clean and confortable, with good heat (they have A/C too but did not try it), LCD TV (nice surprise), fridge, coffee maker, and all the usual motel features.
The town of San Rafael (the motel is right in it - we walked - about a half mile to the main area) is charming with lots of things to do and restaurants to eat at.
You can't go wrong with this pick if your on a budget.
The Colonial Motel - Great Price! No Lice!.
Strip Motel - the place was clean (carpet is a bit worn), cheap ($45 the night we stayed) had cable TV and was quiet. The town is cute and is about 1/2 mile away.