For prototyping and small scale manufacturing: Seeed Studio, iTead Studio (They both use the same board house)
For manufacturing: PCBcart
I used Seeed a couple of times and iTead once (just to try). They both turned out OK. There were a couple of problems with my friends' boards but either they solved it (like
ground pour creating short) or got a replacement. Quantity affects quality: For the prototype boards I always choose 10 boards which is the minimum. Last year for Make had to design a badge, ordered 100 of those, the sikscreen quality was higher than my prototype runs. Maybe contacting them beforehand to was also a reason.
Oh yeah, contacting them: I contacted them to get the battery holders, they were real expensive over here. They managed to find a dealer and sent the parts with PCBs. Nice thing if you are looking for some parts which are expensive in .jp but does not worth the shipping price of Mouser or
Digikey.