I've been using 3.0 to run my players through the Castle of the Mad Archmage (the pathfinder version which I back port to 3.0 on the fly) and it's been a blast, though I have implemented a lot of house rules.
I've halved the amount of bonus/negative hit points from a high Con score, this is more a personal issue than anything else, though maybe it ties into the DR change. The gelugon has 30 less HP and 10 more DR in 3.0 than 3.5. I prefer this lack of hit points over a hit point bloat, fights that drag on are the worst.
Armours don't reduce movement speed, I just use encumbrance values, and similarly to Yora, dwarves can carry heavier burdens easier.
I've increased base saving throw progressions, for a total of +15 for a good save and +10 for a bad. Though seeing comments here is making me think that I may be approaching this problem from the wrong end. Maybe I will try out lowering the DC of spells/abilities instead.
I've removed skill points. Characters instead get a bonus equal to half their level +1 to all skill on their skill list. They then pick a number of skills equal to their usual skill points per level + Int mod to get a larger bonus in. Giving everyone more skills has been fine, though I'm unsure how I'll handle multi classing at this point.
Feats are something that I've been tackling on a case by case basis, mostly larger numbers, rerolls. or combining feats together, like dodge + mobility.
Special combat actions like bull rushing and disarming do not provoke an attack of opportunity. Players have fun using these options.
All characters can also cleave as if they had the feat.
I've made made item creation a thing everyone can do, meeting prerequisites, just like granting the feats to all characters. I doubt this will ever become an issue with my table, though I can imagine some folk wouldn't like this
One big change that I've made is adjusting experience. I've added an "energy tithe" to spell casters, which is an experience tax. These taxed points go into a "pool" that the spell caster can use when casting spells that require an experience point cost and when making magic items. It forces the spell casters to engage with those spells/systems and keeps them at a lower level. I do not believe that magic by it's nature can be balanced, but I do think that altering experience/level progression is the best way to attempt something like balance. The numbers in AD&D may not have been perfect, but the concept is good. The tax is highest for spell casters who get up to 9th level spells, and doesn't exist for paladins/rangers.
We've also been using the 3.0 psionic handbook and it's been a blast. I adore the concept of using each ability score for its own special power. I haven't found a need to change anything about it yet, though I am applying a (smaller than usual) experience tax on the party's Psion. He'll just have to ink up some psionic tattoos.
I've told my players to not worry about PrCs. I do and don't allow them... I believe putting them in the DMG was correct, putting them in player targeted supplements was the wrong move. I've decided to remove all prerequisites for entry to PrCs, its completely up to the story/game as to when a character can enter.
I also have allowed players to take a PrC at 1st level. One was a drunken master and it was rad. I gave them some armour proficiencies and an improved unarmed attack to make it work. I think there are a lot of cool, but specific, ideas in many PrCs and playing around with that is fun.