Ahh, this thread again. Well, I'll throw the two cents I do on this thread when I see it to give 10 quick ways to balance a large amount of the imbalance people seem to see in D&D 3.x. It won't cover everything of course, but it will get you on the right track for the most part to prevent the most egregious faults... Warning: I haven't done a lot of updates on it since the last time as I haven't been playing much 3.x recently. :
1.) Get rid of the Spell Component pouch, make Eschew Materials and Natural Spell into Metamagic feats that works like Still and Silent Spell, and make components count.
2.) Polymorph-like spells requires an appropriate Knowledge check upon witnessing an example of the creature to cast equal to an appropriate DC (that number I would have to look into of course, but somewhere between 10-15 + (1/2HD/1*HD) sounds about right). This check may be made once/level if the creature is encountered again.
3.) Eliminate Celerity and similar spells, and close Conjuration (creation) money loopholes through adding a subclause that makes the products of such spells worthless in the open market.
4.) Make Knock function like Find Traps.
5.) Double the costs to create wands, and do not sell dozens of wands in your local Magimart.
6.) Drop all Flight spells by 2 steps, minimum 1 rd/level. Fly? 1 rd/lvl. Overland Flight? 1 minute/lvl. This one is probably the one I have the biggest problem with, but ehh.
7.) Enforce all rules for spells to the letter.
8.) Use Pathfinder's version of Forcecage.
9.) Enforce localized rarity of spells. I shouldn't be able to get a 'desert' spell from Sandstorm while in the middle of the frozen tundra. Subset: Allow only 1 spell/level to be from a regional book. Same rules for Sorcerers and all other casters (see below).
10.) Priests, Druids, and lower tier groups that gain 'all' spells on their home list get Prayer books/Training Books/etc that function as spellbooks.
Slainte,
-Loonook.