MP4 seems to be more universal in that it can play in a browser as well as mobile devices/iPods/iPhones/etc...
F4V, Adobe's H.264 MP4 content wrapped in container allows for the injection of metadata that can be further used for different types of apps/sites/etc... as well.
FLV, which is MPEG-4 simple profile (divx like) can never achieve the same quality results at th same file/bitrate size. However, FLV requires the least amount of resources on the client machine to playback.
IF you are going to Hi-Def, I would shoot for MP4 unless clients will require metadata injection, then I would look to the F4V format. FLV can't compare quality wise to the others. Just my opinion.
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