D&D Rule of Thumb:
These links are more for reference with the group that plays at my house.
Character Sheets - These are the best ones I could find.
Guenever's House Rules - These are the additional modifications that we have made to 3rd Edition D&D. This also covers odd situational rulings.
Extra Classes - Prestige classes that your characters can use.
Die Roller Stats - Visually see the difference between 3d6 and 4d4+2. Plus get some good math stats too.
Items - Magic items we came across in our adventures. Just a tiny amount of the unique ones. This online reference is more for remembering the adventures than as a good collection of things.
Also, maybe you would be interested in what I've tried to make a large whiteboard as a table coating so we simply draw maps and play on a huge grid.
Pathfinder - An open gaming system based on WotC's d20 open gaming system. You can layer this on top of your existing 3.5 edition campaign. Think of it as a more refined and freer version, where thousands of people helped to make the system better.
System Reference Document - The "open" content of D&D. Basically, the player's guide, DM's guide, etc.
Hypertext D20 System Reference Document - A version of the SRD designed for the web. Spells are cross-linked, and tables are added whenever they are used. All of the open and free content in a nice, web-friendly version.
Pathfinder D20 System Reference Document - Like the one above, but includes all of the Pathfinder rules and has tons of additional content.
Open Gaming Foundation - Lots of new d20 books are now able to work interchangeably. This foundation is spearheading the movement, and is also backed/created by Wizards of the Coast.
Wu Jen - Wonderful Excel spreadsheets covering items, spells, characters, and a very large one that will help generate random monster encounters.
The Alignment System - Thorough site explaining the various aspects of each of the alignments. Includes an alignment test to help you pick the alignment that represents your beliefs.
D&D Helper - Similar to D&D Tools (also on this page), but it does a few more things. Experience calculator, movement, turning undead, die roller, reference tables. All for your Palm.
Class Construction Kit - Make sure new classes and prestige classes seem somewhat balanced. This is version 1.1a.
D&D Tools - Freeware Palm OS program to assist the DM. Experience calculator, time/distance, and turning tables made easy. I have a local copy of version 1.00 and also here's a sneak preview of version 1.02 that doesn't require a separate database.
AutoREALM - Open-source fantasy role-playing mapper software.
PCGen - Endorsed somewhat by WotC, this also helps you create characters. I have no idea how good this one is.
Dungeon Crafter 2 - Free tile-based mapping software for Windows.
- Rules of Adventuring - Follow these rules and you will likely stay alive.