QuickTime movie (.mov) turned out to be an absolutely great format for cross-platform presentations, designed in Apple Keynote (“PowerPoint” of iWork office suite). It works hassle-free on both Mac and Windows, all controls and effects work just like they’re supposed to. Back in my Windows days I remember being afraid of running a PowerPoint 2007 presentation (e.g. designed at home) on PowerPoint 2003 (installed on a computer in the University), now there’s a much bigger difference between Keynote yet no hassle at all.
The only possible downside is that QuickTime may not be installed on the other computer, but installing it on the University computer wasn’t a problem for me.