I think that 3.5E made some significant changes to the way that PC parties play and that's going to affect all the monsters to some degree. Haste, Buff durations, Harm etc all changed and now expectations that were valid under 3E are no longer true.
There was a thread here just recently about the Immoth and whether it was overpowered for it's CR; I felt that it definitely was under 3.5E because its Ice Rune ability seemed to be a counter to the expectation that a 3E party would have Haste. It's things like that I am thinking of; if a monster is balanced to take on a Hasted party casting 4 spells a round then he's going to be overpowered when facing a party only casting 2 times. (Apparently he may be overpowered when facing a 3.0 party, but thats another story.... ;-)
Even at low levels things may have changed to make them more or less effective. A creature that depended on the Darkness-Blindfight combo is now hosed (Yes, I just ran into the new Darkness rules for the first time last night!) So I think you just end up looking at each new monster you are considering to see if his primary tactical ability got nerfed or pumped up under 3.5E in relation to what the PCs will be doing.