$ ffmpeg -i movie.wmv -pix_fmt yuv420p -vf setsar='1/1' vid.mp4
The key difference from the default .wmv -> .mp4 conversion is specifying the pixel format as yuv420p and setting the storage aspect ratio (SAR) to 1:1 (or 1/1). The default using a rgb pixel format and inherites the storage aspect ratio from the source... which may or may not be one to one. The resulting video looks like this:
$ ffprobe -show_format vid.mp4 ffprobe version 1.1.git Copyright (c) 2007-2013 the FFmpeg developers built on Feb 5 2013 07:56:01 with gcc 4.6 (Ubuntu/Linaro 4.6.3-1ubuntu5) configuration: --enable-gpl --enable-libass --enable-libfaac --enable-libfdk-aac --enable-libmp3lame --enable-libopencore-amrnb --enable-libopencore-amrwb --enable-librtmp --enable-libtheora --enable-libvorbis --enable-x11grab --enable-libx264 --enable-nonfree --enable-version3 libavutil 52. 17.101 / 52. 17.101 libavcodec 54. 91.100 / 54. 91.100 libavformat 54. 61.104 / 54. 61.104 libavdevice 54. 3.103 / 54. 3.103 libavfilter 3. 35.101 / 3. 35.101 libswscale 2. 2.100 / 2. 2.100 libswresample 0. 17.102 / 0. 17.102 libpostproc 52. 2.100 / 52. 2.100Input #0, mov,mp4,m4a,3gp,3g2,mj2, from 'vid.mp4': Metadata: major_brand : isom minor_version : 512 compatible_brands: isomiso2avc1mp41 encoder : Lavf54.61.104 Duration: 00:00:17.07, start: 0.000000, bitrate: 1817 kb/s Stream #0:0(eng): Video: h264 (High) (avc1 / 0x31637661), yuv420p, 880x646 [SAR 1:1 DAR 440:323], 1814 kb/s, 30 fps, 30 tbr, 15360 tbn, 60 tbc Metadata: handler_name : VideoHandler[FORMAT]filename=vid.mp4nb_streams=1format_name=mov,mp4,m4a,3gp,3g2,mj2format_long_name=QuickTime / MOVstart_time=0.000000duration=17.067000size=3877456bit_rate=1817522TAG:major_brand=isomTAG:minor_version=512TAG:compatible_brands=isomiso2avc1mp41TAG:encoder=Lavf54.61.104[/FORMAT]
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