Based solely on the campaign setting-independent books (not FR or Eberron books for example), I would say that there is a list of offending items that can be counted on both hands, and maybe require a few toes. Oddly enough, three of the biggest offenders are found in the core rules.
Power Attack
Metamagic Rods
Multiclassing (too good, too easy, and no drawbacks--it should be less beneficial and have more drawbacks)
Sudden Metamagic Feats
Divine Metamagic
Divine Insight
Warblade
Elusive Target
Radiant Servant of Pelor
Frenzied Berzerker
Craft Contingent Spell
Vow of Poverty
Warshaper
Now Power Attack in and of itself is not that bad, but if I take Power Attack off the list of things that I think are overpowered, a number of other things immediately jump on that I have a problem with, such as:
Leap Attack
Shock Trooper
Dervish
Wraithstrike
Exotic Weapon Master
and more...
If Power Attack were just toned down a touch so that it wasn't so easy to add stacking "doubling" bonuses, then I think all this stuff is fine. If the bonuses are limited to "half-double" then that would probably eliminate most problems I have with it.
But overall, I think 3.5 is a well-designed, well-balanced system.