The main reason I didn't convert was (as mentioned above) most of the spellcasting villains rely on Haste as a tactic.
The only encounter that leaps to mind as a *real* problem is the balor.
The group's likely to be in the region of level 15-17 when they meet it. It's CR 18 in 3.0, which is a fair (if challenging) encounter.
In 3.5 it's raised to CR 20 and has some pretty horrific abilities.
Oh, and the zombies. Converting the zombies with 3.5 templates would be dull.