Many, but the first that comes to mind is lIlya utterly freaking out over Miyu's maid uniform, complete with mounting her while wearing an expression◊ that would be more appropriate on a psychotic thrill-killer than a girl who thinks maids are cute. Poor Miyu...
Illya recognizing just a second too late that 'I thought you were my brother' is really not the best excuse for why you just surprise-French-kissed someone.
"RUBY FOREHEAD FLICK!!"
Basically anything Irisviel does whenever she shows up. Anything.
She took out both Illya and Kuro combined with a Forehead Chop.
Similarly to Irisviel, if the scene features Illya's friends from school, it's going to be funny. That's just how they work. Highlights include:
Calming Tatsuko down by putting a bag over her head as though she were a scared horse... and it works.
The net result of their attempts to 'make Illya into an elegant big sister'.
Chapter 12 of Zwei. The cooking duel chapter. The whole damn chapter, barring maybe six or so pages. Particularly any moment Tatsuko is on-panel.
In Episode 4 of the anime, Miyu is having a hard time learning how to fly. So what does Luvia decide to do? She throws her out of a freaking helicopter!
The last third of Episode 1, where the story proceeds to skewer various magical girl tropes, with poor Illya along for the ride while the mildly psychopathic Ruby takes the opportunity to take revenge on Rin. What really makes the whole thing perfect is the brilliant voice acting, never faltering in that sickeningly sweet tone:
Ruby: Very well. Ilya-san, point me towards Rin-san while saying "damn you" in your head!
Ilya: Um... *half hearted* "Damn yoooou..." (Ruby electrocutes the shit out of Rin) AAAGH! IT SHOT SOMETHING!
Ruby: Ilya-san's answer is as follows. "I'm not giving this stick to anybody. Go back to where you came from, twin tailed hag!"