Wong.
FLV (as we know it today), MKV & AVI are FILE_FORMATS, they are containers and they can all contain H.264 encoded video.
I repeat, you CANNOT "take a piece of Media and encode it with" MKV or AVI. They are are NOT codecs. Yes, when FLV first appeared on the scene it was a container format that pretty much always contained a simple interleaved video & audio stream. That is not the case today.
Check out these:
http://en.wikipedia.org/wiki/MKV
http://en.wikipedia.org/wiki/Flash_Video
http://en.wikipedia.org/wiki/Audio_Video_Interleave
And you will find out that a
container is much different than a
codec like:
http://en.wikipedia.org/wiki/H264
Again, new videos on YouTube and Hulu are already in the H.264 format. That is why the iPhone can play most YouTube videos though the YouTube app.