Traps that are 'harder for smart characters' would probably work by having a release mechanism difficulty that scales with the height of the stat. This would be true of physical characters as well, if you imagine a situation where a fighter has to fight a clone of himself, or more to the original point, a wizard has to out-cast or out-think a duplicate of herself.
Alternatively, if you want to really stick it to smart characters who aren't physical, focus on traps that need physical tests to overcome. There's very few ways to outsmart a rock, especially if it's barreling down at you from the top of a tunnel with only one other way out.
I suppose you could also house-rule a specific mark that targets the party as a whole, but directs minions to focus fire on the character with the highest intelligence or wisdom. For instance:
"You open the ancient scroll eagerly, ready to peruse the secrets it holds. A cloud of abnormally potent dust flies into your face, triggering a coughing fit,"
Trigger: Someone in the party opens/reads a scroll.
Target: Creatures in Close Burst 10.
Effect: Each creature in burst is marked with "Mantle-Bane of Intellect".
Bane of Intellect - Encounter.
X type creatures and/or Dominated characters attack target with highest intelligence modifier.
Save vs. Fort - should stick for a while, so possibly multiple saving throws.
Special: On a critical success, the mantle is destroyed, otherwise, the mantle lies dormant in the character until they take a short rest (after meeting the save), otherwise it is passed to another creature with an equal or higher intelligence modifier.
Aura detectable by Arcana if just dust, or Arcana & Nature if made of a magical/psionic swarm.
On fail: "A halo of red light appears, encircling your forehead. As your memories race and you begin to ponder as to what this could mean, it glows brighter."
Fail in combat: "The horde of enemies suddenly eyes you angrily (or hungrily if undead!)."
For added flavor, it could flare brighter when the character makes knowledge checks, uses a tactical power, or uses any ability that comes from memory or mental prowess.
There is also the possibility of a role-playing based trap focusing on how much any character is thinking. Characters have to clear their minds and cease all active thought.
Save has added difficulty set to their wisdom or intelligence modifier, whichever is higher. Each save takes up both HP and Time to try again. This targets everyone if everyone is initially trapped, but obviously only really hurts the brainy ones.
If all else fails, target their reflex and poison them with something that hinders int - they could be your patented "Suddenly Drunk Darts" - on a fail, your int mod is now lowered to Zero. Will not raise modifier. Lasts one encounter.
I apologize if the current way I've formatted my suggestion doesn't fit into how traps are created in current D&D editions. I do not have access to the DM's guide. I'm pretty free to imagine solutions if the things I suggested don't fit, but until I get the DM book, you may have to rely on someone else to codify it.