Hey Pauly,
Thanks for the informative reply, It really is ixactly the type of info that I am looking for. I think I will start out with building the arduino on the breadboard but I may try to take it as far as burning the bootloaders onto the Atmega. I'm going to use your shopping list as a reference for the parts that I need to buy. The adafruit protoboards look good, but I think they went up in price as they are now $11.25 each after qty 10. Ouch! Otherwise, I may just stick with the regular old perfboard.
-Daniel