MOV is a computer file format used natively by the QuickTime. The format specifies a multimedia container file that contains one or more tracks, each of which stores a particular type of data: audio, video, effects, or text (e.g. for subtitles).

WMV is a video compression format which is developed by Microsoft which is developed by Microsoft. Its main competitors are MPEG-4 AVC, AVS, RealVideo, and MPEG-4 ASP. Version of WMV video file including WMV 7, WMV 9.

Quicktime MOV is automatically embedded into the browser on download, whereas wmv requires coded embedding or external application streaming.
MOV is more accessible on multiple platforms than WMV.
WMV tends to compress better, but with new H264 format in Quicktime it's becoming less of a problem.

Other Comparison: 3GP vs 3G2 / MP4 vs FLV / MKV vs MP4 / MP4 vs MP3 / 3GP vs MOV / 3GP vs FLV / M2TS vs MP4 / MP4 vs 3GP

Related Post of MOV File formats

Related Post of WMV File formats