i have found and been using "Any Video Coverter" which is free to use unregistered, and it supports a ton of formats, almost all phone and apple formats, flash .swf, and handles .mkv files, just thought i'd share whilei burn a DvD of "The Dictator" from a rip with it, and have been using it for converting 115MB video files exported from flash for my music into 15MB .swf files for youtube.
I'm mostly using Amazon Elastic Transcoder now. Couldn't get ffmpeg or Super to work :(
k, heard you were having some troubles meeting MB limits, and that's the best software i've used.
Good Luck!