Tinic Uro has posted a lot of information on the new file extensions that will be used by Flash video, given the fact that H.264 encoded content will become more and more popular and important over the coming months.
The primary reason for the move away from .flv for H.264 encoded content appears to be compatibility: Adobe want to ensure that a file with a a certain extension is compatible with Flash. The primary extension for H.264 compatible video in Flash will be .f4v. Other file formats include .f4p for protected media, .f4a for audio files and .f4b for audio books. You may still use .flv for these files (the Flash Player will not look at the extension anyway) but I guess this is discouraged. If you run your own web server then I recommend you add the necessary MIME types now (they are listed on Tinic's site) or ask your hosting provider to do this. I remember many issues a few years back when .flv became popular as web servers did not know how to serve that format in a way that browsers could understand.

More information can be found on Tinic's blog.