I found an excellent tutorial on how to install FFMPEG in Ubuntu 9.04 Jaunty Jackalope. I have been struggling with the correct instructions until I accidentally bumped into this thread in the Ubuntu Forums. The instructions listed here did the trick for me. It not only works for Jaunty, but it has instructions for previous versions of Ubuntu as well. It takes a good 15-20 minutes to compile the source code, so grab a cup of coffee and come back later when it is all said and done.
# ffmpeg -i fifa32.wmv -r 25 -ac 2 -ab 64 -ar 11025 -s 300x200 -qscale .1 -y fifa32.flv