I'm updating some PDFs created in Adobe InDesign file. I'd like to add a video clip to each ID file/PDF, but the clips are currently in WMV format, which is unsupported.

ID will take SWF, Quicktime, and AVI, and my audience is 99.9 percent PC-based, even though I'm on a Mac.

For problem-free conversion and playability on a generic PC, which would be the best format? Thanks.

Probably Flash. That's the standard for Web video, or at least one of the bigger ones. The other is h.264 in a QuickTime wrapper. Files with be somewhat larger with h.264, depending upon compression levels but you might get higher quality video with less artifacts out of this option.