I think the best would be to export your videos to FLV extension as Flow player pretty much handles that the best.
Don't blame Moodle for mp4/m4v files because HTML5 is not supported the same on all browsers. I know that IE9 doesn't support HTML5 at all.
You'd have to hope that all of your students have quicktime installed and that's a hassle. So take your mp4 and run them through anyvideoconverter (http://www.any-video-converter.com/download-avc-free.php) this will convert them to FLV.