Links

Technical data

6500 Microprocessor Family Programming Manual - the official manual for programming the 6502 series, in HTML format.
Commodore 64 Programmer's Guide - the official programming manual for the Commodore 64, in ASCII text format. Chapter 5 is a gentle introduction to machine language and the CBM KERNAL library, and duplicates a lot of the reference tables from the 6500 Programming Manual above. - the other chapters cover graphics, music, sound, input, and BASIC programming. If you're targeting the C64, you need this file.

Computerbrains: Home of CCS64, an obscenely accurate Commodore 64 emulator. This can run .PRG files directly. This is the best Windows emulator I've found.
VICE: The Versatile Commodore Emulator. Emulates many CBM machines, and runs them on nearly anything. CCS64 is marginally more accurate, but VICE is very, very, good. It also runs under Linux.
FCE Ultra: Currently the most accurate, highest quality NES emulator for Unix or Windows.
Apple II Oasis: An Apple II emulator for Windows that seems to be well regarded. I know little of Apple II, so this is my best guess as to the emulator you should use.

Python.org: If you don't have Python, you can't run P65-Ophis. Get it here.
Perl.com: If you don't have Perl, you can't run P65. Get it here.
6502.org: A very nice resource for the 6502 processor. If you're writing code that doesn't target one specific 6502-based machine, look here first.
C64.org: Core page for the C64 scene.
NESdev: A collection of documents on NES development and emulator development. If you need NES information, check here before you hit Google.
Zophar's Domain: an emulator resource page. Worth exploring, especially for non-PC emulators.