Handbrake for the Mac is great. Take a look at visualhub. This multi-encoder honestly eats everything, from WMV to flv etc. and it exports everything, is easy to use and if you own more than one MAc, you can form a grid with some clicks so your macs can share the encoding work between them. A gem in the Mac encoding world.
find it here... VisualHub: The Universal Video Converter for Mac.