Yes, well, at the time I didn't have the ability to mass-produce professional revisions of the core rules, so I sort of had to allow the spells in the PH on principle. I had one weasely player in my campaign who always cast glitterdust, evard's black tentacles, web, and grease in every single fight. While I didn't see fit to ban core spells (though I did ban the 3.0 Evard's as too much of a PITA), I let frowns and "oh, gee, grease again!" comments let the player know that I'd appreciate a little more creativity and less reliance on broken/overpowerd rules exploits.
I had another player--Jason Bulmahn--whose eye for rules, long RPGA history, and overwhelming competitive spirit immediately made him hone in on the most powerful stuff. I'd look at the spells Jason chose very closely, since his understanding of the rules and personality led him to borderline stuff almost naturally. To his credit, the powerful stuff he went for ALWAYS supported his character concept, which came first and foremost even to the point of making willfully bad meta-game decisions simply to stay in character. So I didn't ban a lot of his stuff, but I watched it very closely.
At the time the spell that bothered me the most was the one that let you use a swift action (relatively new at the time) to "oh no you didn't" immediately cure damage. At the time I greatly resented the way that this took narrative control away from the DM, and felt it was an affront to the story of the game, which is more important to me than the rules. I strive to avoid having to "rewind" during the game as much as possible, and really hated the way these spells made me eat words I had uttered only seconds ago.
I have mellowed out considerably on the topic of swift actions, but that spell and others like it were probably the genesis of my general dislike of that book.
Actually broken spells sealed the deal.
--Erik