www.6502.org - An invaluable resource on the MOS 6502 processor. Has links to information on everything you could possibly want to know about it.
The Incredible 6502 - Has some great textual documentation on the 6502, as well as an instruction set summary, list of machines that use the chip, and more.
Dan B's 6502 Tech Page - Contains pages that describe the instruction set, and has op code table lists by instruction and opcode.
6502 Instructions - The most descriptive and useful instruction set reference I have seen. Was an priceless resource when writing emulation code.
6502 Cross-Assembler xa65 - This is the cross-assembler we used to make 6502 objects under cygwin.
Cygwin - A Unix environment for Windows that we used to run the cross-assembler and tools.
The Xmodem Protocol Specification -This is the communications protocol we used for sending a binary from the PC to the Atmel over a serial port via Hyperterm.
www.asciitable.com - This site gives you everything you need to know about ASCII.