I've seen three things that have raised eyebrows in my group.
1) Owl's Insight, the 5th lvl druid spell that gives you a major enhancement bonus to Wisdom. A single-class 19th lvl cleric PC gained access to the spell via Miracle, used divine metamagic to make it persistent... and then took a single level of monk. Suddenly, his spell DCs are berserk and his AC (with no armor) is beating out the party fighters. Now, admittedly, the divine metamagic feats fill me with sick dread... but even without persisting it, the huge enhancement buff is ripe for broken-ness. Potentially gaining +5 or more to your spell DCs is huge. I'd prefer they just stuck with Owl's Wisdom.
2) The Orb spells. I don't think they're broken, but they're good enough that nearly every mage of any kind that I've ever seen since their release has at least one. It's the one true failsafe. No save, no SR. All you've got to worry about it energy resistance and your attack roll. As a DM, though, I'm okay with them.
3) Ruin Delvers Fortune. This is the one that I'm closest to nerfing, although I'm loath to nerf spells. Not because it's necessarily overpowered, but because *every* player in my group (that's eight people...) now considers it mandatory. For the last 9 months, every sorcerer (or similar) in the group has taken this spell. The typical statement I hear is: "If stoneskin didn't have a material component, there *might* be some competition... but as it stands, any PC who even vaguely cares about his character must take this spell. End of story". Now, my group is pretty diverse - roleplayers, rollplayers, munchkins, and guys who are really just there to eat the pizza. But when everyone agrees that it's the first and only spell to take at 4th level, it worries me... because it's limiting diversity.
...oh, and for the record, there is only one spell from a 3.5 WotC source that I've ever actually banned in my games: Shivering Touch, from Frostburn.
3rd level Wizard/Sorcerer. Touch. 3d6 Dexterity damage. No save. It's ability damage, unlike the Strength penalty caused by Ray of Enfeeblement. Even without a Lesser Rod of Maximize (or similar), that will take down most "big" creatures in one shot. Conceivably, if you can beat it's SR, it's an insta-kill (no save) against a Great Wyrm Red Dragon (which, worse yet, takes +50% damage because of Cold subtype vs Fire subtype).
If anyone can find a flaw in the above analysis, or can point me to errata, I'd be much grateful.
