If you prefer command-line you can use ffmpeg (or handbrake-cli).

MP4

Assuming you're using a recent version of ffmpeg:

ffmpeg -i input -c:v libx264 -crf 23 -preset medium -c:a aac -b:a 128k \
-movflags +faststart -vf scale=-2:720,format=yuv420p output.mp4

• -crf: Quality. Range is logarithmic 0 (lossless) to 51 (worst quality). Default is 23. Subjective sane range is ~18-28 or so. Use the highest value that still gives you an acceptable quality. If you are re-encoding impractically large inputs to upload to YouTube or similar then try a value of 17 or 18 since these video services will re-encode anyway.

• -preset: Encoding speed. A slower preset provides better compression (quality per file size) but is slower. Use the slowest that you have patience for: ultrafast, superfast, veryfast, faster, fast, medium (the default), slow, slower, veryslow.

• -movflags +faststart: Allows video to playback before it is completely downloaded in the case of progressive download viewing. Useful if you are hosting the video, otherwise superfluous if uploading to a video service like YouTube.

• -vf scale=-2:720,format=yuv420p: A filtergraph using scale and format video filters. Scale to 720 pixels in height, and automatically choose width that will preserve aspect, and then make sure the pixel format is compatible with dumb players.

• -b:a 128k: Audio bitrate. If your ffmpeg is outdated then you'll need to add -strict experimental to use -c:a aac.

MOV

Since your MOV and MP4 files probably contain the same video and audio formats you can encode the MP4 and make the MOV by re-muxing (with stream copy mode) instead of re-encoding:

ffmpeg -i input.mp4 -codec copy output.mov

WMV

FFmpeg only supports WMV 7 and 8. I am unaware of an open source encoder for version 9.

$ ffmpeg -encoders | grep -i windows
[...]
 V..... = Video
 A..... = Audio
 ------
 V..... wmv1                 Windows Media Video 7
 V..... wmv2                 Windows Media Video 8
 A..... wmav1                Windows Media Audio 1
 A..... wmav2                Windows Media Audio 2

As I am unfamiliar with these encoders I can only give an untested example:

ffmpeg -i input -c:v wmv2 -b:v 1024k -c:a wmav2 -b:a 192k output.wmv

Getting ffmpeg

You can download a Linux build of ffmpeg or follow a step-by-step ffmpeg compilation guide to customize your build.

Using a bash "for loop" to perform a batch encode

To encode all videos in a directory:

$ mkdir encoded
$ for f in *.avi; do ffmpeg -i "$f" -c:v libx264 -crf 23 -preset medium \
  -c:a aac -b:a 128k -movflags +faststart -vf scale=-2:720,format=yuv420p \
  "encoded/${f%.avi}.mp4"; done

Also see

• Who can tell me the difference and relation between ffmpeg, libav, and avconv?
• FFmpeg H.264 Video Encoding Guide
• FFmpeg AAC Audio Encoding Guide
• Using HandBrakeCLI

Matroska (MKV)

This will stream copy (re-mux) all streams:

ffmpeg -i input -map 0 -c copy output.mkv

The -map 0 option is used to include all streams. Otherwise it will use the default stream selection behavior which would only result in one stream per stream type being selected. Since Matroska can handle most arbitrary streams I included -map 0.

MP4

This will stream copy (re-mux) all streams:

ffmpeg -i input -map 0 -c copy output.mp4

• If your inputs formats are not compatible with MP4 you will get an error.
• Your player/device may not support all arbitrary, less common, or legacy formats even if they are supported by MP4.
• If in doubt re-encode to H.264 + AAC as shown below.

This will re-encode the video to H.264 and stream copy the audio:

ffmpeg -i input.ts -c:v libx264 -c:a copy output.mp4

The next example will re-encode both video and audio:

ffmpeg -i input.ts -c:v libx264 -c:a aac output.mp4

Lossless H.264 example:

ffmpeg -i input.ts -c:v libx264 -crf 0 -c:a copy output.mp4

Lossless files will be huge.

See FFmpeg Wiki: H.264 for more info.