Very few have I really banned, but many have been altered or changed or are going to be altered.... at some point...
Shapechange 3.5... I might ban it. It does really scream 'FIX ME!,' but after a few threads here about the spell, I'm less inclined to think that it is really that broken. But I'm still on the fence about it, but I probably won't use it as-is.
Gate - Haven't banned it yet, might fix it to HD no greater than the caster level or some such. Hasn't come up yet.
Mordenkainen's Disjunction - Haven't banned it. Told the players outright that it's more of cold war kind of thing. No one wants to risk having all their pretties destroyed, so no one will use it against you until you start using it. It's just such a cheesy spell.
Haste 3.0 - Didn't ban it, just had enemy spellcasters use it against the party more. I almost killed a 10th level PC wizard (who had been abusing haste for 5 levels...) with a flying, hasted, invisible wizard of 7th level. Thankfully, 3.5 came out and I started using the new haste right away. God I hated 3.0 haste...
Miasma - Banned the 3.0 version. Haven't touched the 3.5 version.
Shield - Took me using 3.5 to realize how stupid 3.0's version was. Never banned it though...
Firebrand - Never banned it, but I probably will never allow it in a game again as-is.
Mass Fireshield - Looks pretty powerful for 5th level, haven't banned it yet though. I'd like o see it in action first.
Summon Undead - Definitely needs a fixing as the LM version is pretty much a straight up cut-n-paste from 3.0. Won't ban it, but I'll fix it as I really like the spells.