Here is a sample command line to be used with ffmpeg which is based on whats doing HTML5 Video Maker on the background.

ffmpeg -y -i "input_video.avi" -f mp4 -strict experimental -vcodec libx264 -crf 22 -profile:v high422 -level 4.0 -pix_fmt yuv420p -movflags +faststart -acodec aac -ac 2 -ab 128k -ar 44.1k "output_video.mp4"