Chris Ward's 6502 Computer System - System/65 owes a huge amount to this guy's project, which served as both the inspiration to do a simple, no-frills system before trying to tackle my dream projects and a guide for more of the design details than I really care to admit. I think my case design is cooler, though.
Magic-1 Homebrew CPU - Some day, I will be as cool as this guy, for whom building a homebrew computer with an existing CPU apparently just wasn't good enough. Yes, he actually built himself a CPU out of TTL components, then built a computer around it. Tune in next week, when he constructs one out of stone knives and bearskins!
6502.org - A very comprehensive resource on the most popular 8-bit CPU that wasn't the Z80. Lots of information and sample code to be had!
6502 Macroassembler & Simulator - A very, very useful tool for writing and debugging 6502 code. Windows-only, but does offer the source code.
N8VEM Discussion Group - Seemingly the only homebrew-computing discussion group on Google Groups. While certain members will try to talk you into purchasing an N8VEM board every time you ask a question, they're a knowledgeable and friendly bunch who helped me figure out a number of things about the System/65 design.
DOS/65 - A CP/M workalike for the 6502. Somewhat limited, but worth a look.