If you need to play back video clips in a presentation with the highest possible confidence nothing will go wrong, use PlaybackPro.
If you can’t use PlaybackPro, use Keynote.
If your only option, however, is PowerPoint running on a Windows laptop (as it was for me this week), most combinations of file formats and codecs won’t work. This was the ffmpeg command that worked best:
ffmpeg -i input-video.mp4 -q:a 2 -q:v 4 -vcodec wmv2 -acodec wmav2 output-video.avi
Note that even though the windows media codecs were used, I had the best luck with putting it all in an avi wrapper. Just for completeness, this was working in PowerPoint 2010 on Windows 7.