I think my two personal favorites have to be...
There's a point in the Dead Money DLC where Christine tries to explain to you through her hand motions that your collar and her collar are at just the right frequency so that they'll jam incoming signals for a while. If you lack INT or perception but try to make the check anyways, you're character will say, as if he were practicing his best Homer Simpson impersonation: "Aaaah, I understand. The collars are explosive."
Another one is you can offer to give the Legion advice on how to deal with landmines. If you lack enough experience with explosives, it leaves your character saying "The key is to approach the landmine, veerrrry carefully." The response you get is something along the lines of "Oh really genius? Why don't you go test that theory out for us?"