I mostly use froggy1's xvidenc script (my PC's are too old to process H.264 with any sort of reasonable speed ... I'm waiting 'til I get a new pc before I use his h264enc script
).
I also use avidemux for some files.
For creating dvd compliant mpegs I use tovid, which I believe uses both mencoder and ffmpeg. ( not sure if it still uses mencoder ) .
For Non-Linear-Video editing, I use kdenlive, which uses ffmpeg.