SWF is a vector graphics file format which developed by Macromedia and Adobe systems for multimedia, vector graphics and ActionScript. SWF files can contain animations or applets of varying degrees of interactivity and function.

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).

SWF is widely used for displaying "animated" vector graphics on the Web, while MOV is used for Apple QuickTime.
Both SWF and MOV are lossy formats which sacrifices quality for file size.
Apple devices and software like iPad, QuickTime, iMovie, etc support MOV files, but do not support SWF.
MOV is the industry standard with better quality and has more widespread support than SWF.

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

Related Post of SWF File formats

Related Post of MOV File formats