The wizards current favorite tactic: Find the enemy mage or nastiest opponent if no mage and polymorph other him into a snail, goldfish, turtle or other basically helpless critter.
Some creatures are immune to polymorph. Undead and constructs are immune to all effects calling for a Fort save, which is both polymorph and a lot of your other all-or-nothing spells. If you make the undead nasty enough, like high-level vampires or a lich, then the cleric's turning won't be that effective (and from the sound of things, I'm guessing he hasn't put too many feats into boosting it).
Also, I think some types of shapeshifters may be able to get around polymorphing by just resuming their natural form, but I don't have any rules to quote you.
I think a lot of it just comes down to a question of how much you want to meta-game the foes. Granted, not every encounter in the world is going to be specifically tailored for the PCs, and the enemy won't always know the party's capabilities. But if they've got this entire cult (or whatever) after them, and all kinds of people being sent out, then there's a good chance the organization is familiar with their tactics by now. So it does make sense that the other side would be more prepared for them.
As a side note, I've found that, more than CRs or equipment or anything else, knowing what you're about to fight and being prepared is generally what determines the way the fight is going to go.
Consider this idea: the bad guys get tired of loosing henchmen to the PCs and decide to contract some outside help. They find a group of vampires, formerly an adventuring party, with class levels around 6 or 7 per person. These vampires are under an unusual curse- they can't survive on normal blood, it has the be the blood of powerful people, ie those with higher levels, more magic, etc. Therefore, the group hires itself out as assassins to evil organizations who want to get rid of pesky heros, earning both blood and gold.
Classes are up to you, of course, since you know your party best. I'd suggest at there be a cleric to heal/buff the bad guys, and of course your typical assortment of fighter types. And then, a specialist abjurer. I had a PC playing one IMC, his entire purpose was to deny spellcasting to the enemy. With a load of dispels and a couple of counterspelling feats from the FR books, he was generally able to prevent one or two spells being cast per round.
One thing to remember is that, if you're going to use undead, the party rogues will be next to useless without their sneak attacks. Hopefully they have ways of distracting the bad guys without those abilities, or you could throw some non-undead in there- but expect your wizard to make quick work of them.
