What is the best way to make Windows compatible with .MOV format?
.MOV is a container format, not a video format. As such it can contain media in any number of 'tracks' of audio, video, subtitles etc. In particular, video tracks may use any supported codec, not just Apple-specific ones. It's very common to see H264 encoded video in a MOV file, and H264 is widely supported on Apple, Windows and Linux platforms.

So if you control the encoding, use H264 and you'll have nearly universal compatibility. If you don't control the encoding, you have to insure that the target system supports the codec used, which puts you in a bind because there are dozens of codecs and a given system may not have yours installed.