D&D 3.X, for me, required massive house rules. Some of them, luckily, were foreseen and provided by 3rd party publishers, and others I had to create myself.
* It was critical for me to decouple skills and feats from level, so that a character could gain additional skill points (and in some cases feats) out of level sequence. While this means that it is harder to gauge challenges, it also means that the expert blackmith need not be high-level. And it means that I can make quick-n-dirty NPCs without having to worry about the math.
* It was critical for me to have monsters that can both (a) effectively challenge the party, and (b) not risk a TPK. My solution to this was two-fold. One one hand, PCs can earn APs by meeting session-specific goals that they set. This gives them a measure of plot protection. On the other hand, I use a WP/Vitality system so that a creature which is unlikely to kill you can still potentially cause you harm. Further, the power curve in 3e is so steep that a monster which threatened a TPK at one level wasn't even worth considering a few levels later. Therefore, both reducing the power curve and breaking down the monster design system were important to me.
* I dislike the "ever class is a superman spellcaster" syndrome that exists in 3.x (and, apparently, will be even more prevelant in 4e), so I rewrote non-spellcasting versions of some classes, as well as re-writing nearly every class to make options match the flavor I was after.
* I considered PCs taking "turns" that take place at multiple scales, including the seasonal scale, so that characters can accomplish things during downtime....and that encourage taking downtime.
* I wrote legacy rules allowing the players to increase their PC's capabilities or change the setting in some way. I wanted to encourage long-term investment in the setting.
* I rewrote epic feats, and made it possible for a PC as low as 5th level to take one by using his legacy for that purpose.
* I made progression slower.
* I reintroduced risk to magic, and included a couple of additional magic systems.
* I streamlined parts of combat, and made other parts more granular, resulting in a combat system that IME is both significantly faster and replete with interesting choices for the PCs.
* I added granularity to some things that I thought were glossed over too much in the RAW. For example, the creation of magic items.
* I rewrote all of the races, including humans, and broke them down in terms of subrace, with various three-level racial classes helping to differentiate (say) the Viking-like Ska from the psuedo-Indian Varanamen, and to differentiate both from Lakelanders, Indrus, and other human groups.
* Elves and gnomes became fey, with adjusted rules from The Complete Guide to the Fey making this distinction more meaningful. Dwarves became giants.
* Etc. In all, my house rule document is over 600 pages long, and completely replaces the PHB and part of the MM.
RC