HandBrake

Install required packages

mingw-get install msys-wget

mingw-get install msys-unzip

Install HandBrake

wget http://sourceforge.net/projects/handbrake/files/0.9.5/HandBrake-0.9.5-Win_CLI.zip

unzip HandBrake-0.9.5-Win_CLI.zip

mv HandBrakeCLI.exe /c/dropbox/bin/

Use
Get subtitles

handbrakecli --input input.mkv --title 0

Encode video

handbrakecli --input input.mkv --encoder x264 --quality 23 --rate 23.976 --strict-anamorphic --subtitle 1,2 --output output.mp4

References:
handbrake.fr