They made a Mudd joke in the film--they confiscated that trading ship during the "Mudd incident." I guess the prequel comic has some more references.

Aside from the Klingons, I want to see less villainy and more of the other bits of the show--I'd love to see some stuff with the Horta. And I admit, I'm curious to see how they'd handle an "Amok Time" storyline Given that the Vulcan population is so small at this point, that could be interesting.