Eh, Eagle in this day in age? If you're going cheap, I'd stick with KiCAD. It's unintuitive, like GIMP vs Photoshop, but gets the job done with no restrictions on functionality. I've also heard decent things about CircuitMaker, but never used it. If you have any academic links at all though, or don't mind piracy, I'd grab a student edition of Altium Designer. Solidworks too if you can get it for mechanical modeling.…
What are some of the reputable "small board-houses"? Any recommendations?
I also like macrofab if you want something assembled.
A few times I have ordered from the board houses on Ebay. Like $20 for 10+ boards and they come in about 2 weeks.