Flash should support several other formats
"Flash Player now supports video compressed in H.264 (MPEG-4 Part 10), audio compressed using AAC (MPEG-4 Part 3), the F4V, MP4 (MPEG-4 Part 14), M4V, M4A, 3GP and MOV multimedia container formats, 3GPP Timed Text specification (MPEG-4 Part 17) which is a standardized subtitle format and partial parsing support for the 'ilst' atom which is the ID3 equivalent iTunes uses to store metadata."
- http://en.wikipedia.org/wiki/Flash_Video#Format_details
I was using JW Player to play my audio as MP4 before, so most of the audio I've built up so far is in mp4. Trying to load them with the soundinterface plugin crashes my browser though. Not sure whether there are any plans to invest more resources in the soundinterface plugin, but personally I would love it if it could handle mp4 files.