As for the .flv format..as mentioned by gparis, it is by far the most widely used video format on the Web. It is a container format... meaning it is not a video compression codec but it is a container or "box" that contains both a video file and an audio file, the primary use of which is the delivery of video of the Web.
If your project is designed to include other formats, you may want to do some research into "ffmpeg" or "PHPMotion" to do the conversion if the videos are to be user submitted.
Best wishes,
EfV