Excellent GUI for transcoding needs, very powerful, lots of features, you can tweak (almost?) any of eg. x264's, Xvid's options, AviSynth-based encoding and filtering gives room as much as your imagination can come up with, and it uses the best tools in business!
A bit of a learning curve, but well worth it when you can have the latest bells and whistles to transform your whole media collection into pretty much any kind of usage scenario there is.
Updated regularly, and it keeps track of all the needed tools so you don't have to worry about old versions or incompatible tools.
I've used this for years, and can't remember a single problem in all that time.