Mechbunny's Tube Script can transcode from almost any video format into x264/mp4 via either ffmpeg or HandBrake (as of V6.0.0). This means you or your users can upload just about any format of video to the script and it will convert it to MP4, which can be streamed to all modern desktop and mobile devices such as phones and tablets.
FFmpeg is the leading encoding software available on linux. It is highly portable and works on just about any platform or linux distribution. It is a very fast video and audio converter that runs from the command line interface on your server and able to decode, encode and transode even the most obscure ancient formats all the way up to the cutting edge of video codecs. FFMPEG is free, open source software.
HandBrake is an open-source, GPL-licensed, multiplatform, multithreaded video transcoder. Similarly to FFMPEG, It is a tool for converting video from nearly any format to a selection of modern, widely supported codecs.