I've been looking at this myself recently, for an even smaller run of quantity 50, and found a couple of good options.
1. Smart-Prototyping (China): http://smart-prototyping.com/Prototypin ... rototyping
They will make the PCBs, procure the parts, assemble everything, and also flash it and test it if you wish. The cost for assembly is determined by simple formulas shown on their web page, so you can calculate it yourself before even talking to them. For my medium-complexity board with a mix of SMT and through-hole parts, the cost of assembly for quantity 50 was $7.75 per board. That includes the stencil, but not the cost of the PCB itself or the BOM parts. There is no NRE fee or other setup fees. But they charge an extra 4.4% on top of the quoted price to cover PayPal fees, so it's really like $8.09 per board. This price is with no testing.
2. Microsystems Development Technologies (California): http://msdus.com
Same as Smart Prototyping - they make the PCBs, procure the parts, assemble, and (optionally) test. For my board in quantity 50, the cost of assembly was about $14 per board. Hard to say exactly as they quoted a total price per board, without separating out the PCB, BOM, and assembly costs. This includes a $250 NRE free. For quantity 100, the assembly cost dropped to about $8.40 per board. Again, this price is with no testing.
I chose to go with Microsystems Development Technologies, even though they were more expensive, because they're local to me and the owner was pretty helpful in answering my noob questions. But Smart-Prototyping was also pretty good about answering questions, and I might go back to them in the future if I need more larger assembly runs.
My advice is to be prepared when you talk to manufacturers, and don't waste their time. The overhead of exchanging multiple detailed emails with you to answer questions could easily eat up their entire profit on a small order. Make sure you have a detailed bill of materials with the manufacturer's part number, package type, voltage ratings, tolerance, and Digi-Key ordering link for every part, so they don't have to waste time trying to understand what you intended. I think you'll get a better reception that way.