Well, for one, consider SMT leads. That keeps the top side open.
Consider some via-in-pad process. If you're doing it by hand, it probably doesn't matter, put on enough solder paste and flux until it works. Ideally, you want:
- Untented vias. Gas can escape through the via, rather than trapping a bubble under the joint. Will probably wick some solder, making questionable joints.
- Shut or capped vias: may be more expensive. Does not trap gas, so is fine.
- Capped and plated vias: preferred, but expensive -- the capping process takes time and manual labor, and the overplating takes extra steps.
- HDI (high density interconnect): preferred. Not expensive in quantity (cellphones are a huge user), but maybe not what you want for a few protos.
There may be other middle-grounds, like blind or buried vias. A 4 layer stackup with 2 x 10 mil cores can be drilled for L1-L2 and L3-L4 vias, then glued up to make the final build. (Or they still assemble it as normal and blind-drill before plating? I forget.) Blind vias obviously still trap gas, but not as much as full-height tented vias, and maybe that's good enough.
Laser-drilled vias can be smaller than mech. drilled, and may end up plated shut (good). Not sure how much cost differential that is, honestly. But keep in mind, any discussion of cost difference is basically moot when you're talking a custom proto run in small quantity. You can spend $500 easily.
You might need blind vias anyway, just to route things. A full height via blocks everything on all layers, a real PITA for high density layouts. I don't know if you'll need enough IOs that a 4 layer build is impossible, but you can easily need 6, 8 or more layers.
Keep this in perspective: those cheap $10 runs are mainstream, huge throughput, carefully optimized processes. Every thing you do differently from that process, adds cost. And not arithmetically, but geometrically. A few things -- 2oz here, 1mm laminate there -- are common enough that they usually have optimized processes with little additional cost, but going to a custom stackup, precision drilling, capping, plating, all that stuff -- it goes up quickly. On the upside, you're at least paying enough to get good quality and customer service (something you definitely aren't getting on $10 protos!).
Tim