I'm not totally familiar with the 4pcb (or Advanced Circuits for that matter) pricing model, but I'm sure their turn around time is better than BatchPCB. One thing about BatchPCB is that if you have several small boards (4 is a good starting number) that you need to have made, but don't mind waiting a while, you can get them really cheaply. For example, I have designed several useful devices in 1"x1" of board, which is $2.50. There is a $10 surcharge per order, so as long as you have a couple of these it's very economical. The price increases at the $2.50/in^2 rate, so when they get larger it can become expensive. The few times I've made larger boards they get into the $20 range fast. I've been quite happy with the service, though.
With 4pcb they let me define the turnaround time and would charge accordingly. I don't know their pricing model exactly but it seems competitive especially since they give generous discounts for academia or government projects. They gave us a couple free boards since we put their stickers on our robot which now appears in photos all over the internet; talk about free advertising.
Too much work but if you want then click on schematic & eagle file for open source autopilot ( diydrones and sparkfun ) site , most if not all publish them.Schematic here is an example from spark fun( click on links under documents)
You're getting a bargain ordering it from diydrones. They have (semi)mass production on their side. Producing it yourself is going to cost the same if not more, even if you're using Batch PCB and you're not factoring the amount of time and hassle mounting all those surface mount accelerometers and gyros will cost you + troubleshooting when it inadvertently doesn't work right.
Express PCB, Sunstone Circuits, BatchPCB. They all are approximately equal on quality. I use Sunstone when I need it fast and BatchPCB if it's something I'm not too worried about.
Home etching boards is great for people who do not value their time or sanity and who enjoy keeping vats of nitric acid laying around and permanently staining their sink.
Surface mount is the way to go. Through-hole stuff is quickly becoming obsolete Invest in a quality soldering iron, a heat gun, and a toaster oven and you have a complete surface mount solution.
Even leadless QFN packages with tight pitches are pretty simple when you have the right tools. When rework is needed simply take a heat-gun to the board and everything becomes butter. I've even removed the big TO-252 style MOSFETs on the ESCs with the heat-gun without melting the wire next to them. 30 seconds of heat and you can pick things off with tweezers like they weren't even held down.