Of course there are many more emulation docs out there than I have here. If you happen to have a particularly good doc, feel free to send it to me.

Nintendo Entertainment System Architecture Version 2.1 Marat Fayzullin	This is a detailed, and yet incomplete description of the architecture of the NES system. There is info on interrupts, I/O ports, PPU memory, hit/VBlank bits, joysticks, sprites, and memory mappers. Music information, however, is unwritten.
NES Documentation Version 1.00 Y0SHi	Well, anyone who knows emulation has heard of the Y0SHi Docs. This is a wonderful text on the NES system.
NES Mapper Document Version 0.80 \Firebug\	This is a nice document, done by \Firebug\, that contains information on many of the NES mappers. Including the extended mappers, and seems to be very accurate.
Nintendo MMC1 Matthew J. Richey	This doc provides information on Nintendo's MMC1 chip
Nintendo MMC6 Version 0.2b Fanwen Yang	This doc provides information on Nintendo's MMC6 chip

Rom Hacking

Rom Hack Document Version 1.03 Demi	A good document written by Demi. Based on editing graphics and text in NES roms. It is a good doc, if you plan on doing any rom hacking at all, you should read over it.
Rom Hackers Bible Version 0.2 SerialKlr	This document covers utilities needed for basic rom hacking, how to use them to do text and graphics editing. It also goes fairly deep into the nintendo system itself, including sprites, memory mappers, and general architecture, among many other things.
How to start hacking your own ROMs Kasady	This document is aimed at beginners. It takes you through the basic first steps of rom hacking, and gets you started. For advanced rom hacking this won't cut it, but it is an excellent stepping stone.
Graphical Editing
Palette Color Modifications of an NES file Version 1.8 aStROcReEp 2000	This doc is about, of course, how to modify the palette color of an NES file. It goes throught the process of altering the palette of a nintendo ROM.
The Palette Hacking Doc Toma	This doc explains how to modify the palettes within an NES game.
How NES Graphics Work: The Basics author unknown	This doc is the basics of how NES graphics work, but don't let that fool you. The doc is actually quite complicated, not for beginners. It is, however, a fairly straightforward resource, if this is what you seek.
Text Editing
Changing a NES Game's Text Version 2.0 aStROcReEp 2000	This document deals with changing an NES game's text. This document simply goes over the process of altering the text within a rom, and explains it step by step along the way.
Basics of Rom Hacking Version 1.0 CaTaclysmX	This document is, obviously, aimed at beginners, and deals mainly with text replacement. It also includes information on what tools to use, and how to use them. It deals with both NES and SNES editing.
The Madhacker's Guide to NES Pointers Version 1.1 MadHacker	The reference for any and all pointer tables in NES roms. Taa daa.

Miscellaneous

NES Game Genie Code Format Version 0.71 Benzene	This doc explains the format of Game Genie codes. It includes how to decode both 6 character and 8 character codes, and how these are converted to addresses within the rom.
FFIV Save State Hacking Version 1.0 Jair	This doc explains how to hack your save states from the game Final Fantasy IV in order to change values for various aspects of play.
Metroid Map Data Version 1.0 SnowBro	This doc explains how to hack your save states from the game Final Fantasy IV in order to change values for various aspects of play.