For wizards, limit spells known and downtime. If a wizard gets too many spells available, remember that losing their spellbook is a huge ordeal. The tradeoff for getting to know every spell is that your spells known are a physical object that can be stolen or destroyed.
For clerics and druids, there's not much you can really do without gutting their entire archetype. You can't limit their spells known, but you could limit their spells per day, I suppose...
For Clerics, make sure Nightsticks don't exist in the world. For Druids, harshly enforce the rule that they must know about every animal they want to wildshape into (successful knowledge check, or having seen it, or, most harshly, both).
That still won't stop the most abusive characters from over-running everything else, but it's a start.
The best answer though? Talk to your players about the power of their characters and have them adjust as need be. Be honest with them. Arbitrary limits and houserules can rub people the wrong way. On the other hand, an honest approach and discussion about the problem and possible solutions can foster mutual respect.