I've had these floating in my head for years and I apply them to every job I do, but I feel that it would be good to get them on paper and potentially challenged by the community. (Written in chronological order, as I use them during development)1. Cross Reference EVERYTHING
When you make a polymorph spell, it needs to be checked against all the monsters. All of them. When a new book is in development, every creature needs to be added to the polymorph pool or removed from it (like the sharn)2. Modular Design is GOOD.
This is sort of an extension of #1, but it deserves its own place. A game that has clearly defined terms and keywords can be easily cross referenced and added to without breaking things.3. Iterative Design is GOOD.
If #2 is an extension of #1, then this is an extension of #2. A hardcopy RPG can't go through iterations after release without clunky errata, so all iteration must be during the development phase. The developers of 3.5 weren't testing the game, they were just playing it, and making assumptions that everyone else would be playing it their way. This led to things like the Druid's animal companion being a combat monster, while they assumed a druid would never let his pet get in harm's way.