Thanks for all the responses.
I have done a lot of searching since my post and I will share my findings
There are a few basic players in the processor industry and from what I have seen the PIC and AVR seem like the two worth pursuing (I think i'm going the AVR route).
http://en.wikipedia.org/wiki/Microcontroller had a good explanation of processor vs boards.
I think you can program in whatever language you want if you can find a compiler for it. C seems to be big for the AVR.
Coyote suggested a book but it was more than I wanted to spend, I found one for the AVR thats about half the cost:
http://www.amazon.com/AVR-Introducto...pd_sim_b_img_1