Banned:
Wraithstrike
Rope Trick
Shivering Touch
Mass Resist Energy
Enervation: Until I find how to properly nerf it, it's WAY too good for its level. Energy Drain at level 9 is ok, though.
Energy Immunity (I think that's the right name...it's level 6, in SpC)
Greater Teleport
Mage's Disjunction
Gate
All the "new" polymorph spells that last round/level -- I like polymorph being for more than just combat, and most of these spells...are stupid.
Probably some more from SpC and other non-core books I can't think of right now...
Altered:
Polymorph: Limited to original MM for selections. The Cave Troll taught me to do this. ^_^ To be fair, I also am cautious with using blatantly broken monsters, particularly from MM 3+ (I pretend 2 doesn't even exist).
Shapechange: Also limited to original MM. Thinking of making it cost a small amount of XP each use, instead of the focus. I really don't want to ban or alter the mechanics of such a fun spell.
Haste: Grants extra move action instead of extra attack. Mobile fighters and those that rely on full attacks (flurrying monks, TWF rangers, etc...) seem to like it. I think Haste in general needs a nerf to balance it with Slow, though. Maybe reduced targets. (Slow is save negates, Haste always works, for largely the same mechanical benefits).
Knock: Lets you make Open Locks check (from a Medium range, as normal) even if untrained, and adds your CL to the check. I don't like spells that make skill checks obsolete...
Wings of Cover: Only grant cover bonus to AC, not auto-protection. Still blocks line of effect for spell targeting, may need to fix that, too...
Orb spells: Are Evocations. Still no SR, have found no problem with this.
All "save or die" spells: Leave victim at -9 and bleeding. (ie, 10% chance of stabilizing in time without any help. If Warforged weren't already banned, they'd still be in danger of dying, logic be damned!)
Still working on:
Alter Self: It's just sooooo good for a level 2!
Command Undead