Some of these are from memory - some are from when I was searching to confirm memory.
If you go pre mac - there is an Apple IIc in the sub basement where the reclusive genius lives in the movie Real Genius. (from memory)
Jurassic Park - the first movie - there are Macs in the control room. And although they are shown as the controller systems of the park, aside from a few scenes showing MacOS, the rest of the displays were a different OS (from memory)
Final Destination 2 has a mac (well box at least, don't remember if the Mac itself was ever shown) being carried in a hallway (from search while confirming my memory of Jurassic Park)
Austin Powers Gold Member a Mac laptop is used (from search while confirming my memory of Jurassic Park)
American Pie - kid in love with the super model girl had it in his room that I'm pretty sure was used to broadcast the webcam. (from search while confirming...)
Independence day - Goldbloom used a Mac laptop to display the timer countdown and deliver the virus to the aliens. (from memory)
More modern - the current season of Leverage on TNT - the hacker member of the Leverage team is using Macbook Pros. (from memory, and the fact that I remember seeing them when I watched the episode from a week ago)
And as CrimsonRequiem mentioned - there are quite a few Macs in Japanese Animation, including several series in which the primary characters exhibit hikokimori traits, or are self proclaimed hikokimori - none of which I can name off the top of my head at this very moment, but I have seen them all over in different series, movies, ova's, etc.