I would say that inherently problamatic monsters like dragons, all those spells and basically the fact their dragons, should make them REALLY rare and PCs probably won't see them if they're lucky.
As for the less troublesome monsters like trolls and other "lesser" magical beast, a few tricks are this: any monster with a high DR/magic has it's DR lessened or the magic descriptor changed to a more common thing. Anything like trolls, where regeneration is a problem, alter the rules slightly. For instance, any round in which a troll takes fire or acid damage it may take up to an equal amount of damage from other sources and not have its regenerate ability work for those points.
That is, say the rogue slaps the troll with a torch (essentially a burning club) dealing 4 points of damage that, since it's a torch, is fire damage. Now, the dwarf hits that same troll for 8 points with its great axe. Of those 8 points from the dwarf, 4 are lethal (since "fire club" dealt 4 damage) and 4 are subdual as per regular regeneration rules.
Personally, I think this troll fix is being generous since it's not hard for even low level PC's to come up with fire if they have the extra cash and access to an alchemist to have some sort of "fire bomb" thingy made.