This will be a boring topic.
I'm in the process of going through the 3.0 and 3.5 PHBs and slowly diffing spells that seem to have changed. There are a lot of changes that I missed because I was never looking for them.
Ok, "process" might be too strong of a word. When I take a shit, I reach for a book. Both of those have been within reach recently.
Cone of Cold: I normally have this rolled as 1d4+1 instead of 1d6 per level, in homage to earlier versions. Either is fine, but I remember Joe having an array of blue d4s at some point, and it occurred to me that cone of cold just had to keep being 1d4+1.
Horrid Wilting: This went from 1d8/level to 1d6/level in the switch from 3rd to 3.5. One of my problems with this spell was always that the damage seemed excessive for untyped damage that (of course) can target the PCs but not all of the enemies. But the d8 was charming! It's also one of the few good necromancy attack spells.
Power Word: Stun and Power Word: Blind switched places (Stun became 8th level instead of 7th, and Blind became 7th level instead of 8th). This strikes me as a totally fine change, I guess. Most of my players haven't really played too much with the Power Words because they don't want to be in a situation where they need to use it and the dude has too much health. I think the idea was, stun is more powerful a debuff than blind.
Imprisonment: This spell gained a saving throw, it used to not have one. However, you can now cast it on a foe whose name you don't know (previously you had to know their name and something about them). It's still range touch, and it's still 9th level. I think I like the 2ed/3ed version better, but again, most of the high level dudes didn't mess with imprisoning. You think the 3ed version was broken? This version can actually be used without preparation, on just any random person, whereas the old one could not.
Haste: This one spell is probably the entire justification for 3.5. Probably the most grotesque error in 3.0 world. Of course, now the spell kind of sucks.
Heal / Harm: Harm was probably the second most broken spell. While not every cleric could make a melee touch attack, failing the save took you down to 1d4 hit points. That meant basically that anything that this spell *could* effect, could just flat out die to it. It still can deal 150 points of damage at 15th level and beyond. This is not entirely insane, given the number of save-or-die effects in the game, but given the spell level, I can understand wanting to change it. Heal was the reverse, but again, given the number of death effects that could go on, well, you know. I've personally let Heal scale up to 200 (20th level) since the change, but then the amount of times that that mattered has been pretty small- not so many extremely high level games used this, so I dunno how that plays out.
Forcecage: Previous versions have you tossing away the material component when you memorize the spell, not when you cast it. Current versions have it as a normal material component. Under 3.0, it was undefined how a sorcerer was to cast it (to be fair, it would be a hella rare sorc who would even take forcecage- you have so few spells that you probably want to stay away from ones that cost 1500gp of ruby dust per use). I like the original one better, and I like it as Wizard only, but that's just flavor, and not really important flavor.
Also, it is the matter of much internet debate as to whether it is immune to anti-magic shell (it says the bars it makes are like walls of force, which are immune to anti-magic shell), but 2ed doesn't really hint that it's immune to AMS at all. I've never had this interaction before: I'd assume AMS could breach it.
Here's the overview of changes between 3.0 and 3.5. You'll notice a lot of spells removed from bards (because bards are WAY too strong lol), and some changes that don't make sense (why did we lose two symbols again), along with good changes, and added spells. I'm still uncertain as to whether the 2nd level "animal buff array" (Eagle's Splendor, etc.) are good for the game, as by the high levels everyone seems to have a bunch of these running and it can slow things down.
http://www.wizards.com/default.asp?x=dnd/dnd/20030718aNote that it doesn't bring up the changes to the spells themselves.
Also note that the polymorph changes were big and controversial. The real issue was brought about by using Polymorph Other to do all kinds of crazy shit- even though there was a danger in polymorphing your friend into something that had four arms and was large, true munchkin players laughed in the face of that danger, and then went ahead and bought the quad-wield feats and things went downhill from there. And as we all know, the changes to polymorph solved all the problems, and it didn't require an expository brick in a magazine, and a giant wad of errata, and then a redone errata in one of the Completes, and then a recap in the rules or spell compendium I don't remember which, culminating in the mighty clever fix in fourth edition of "strike it from the game totally". Nope, everything was PERFECT after they changed it for 3.5.
