I've been using TMPGEnc for a while now under 3.0.1 and under 4.0. Here are a few of the things I've noticed about it:
o The installer version doesn't seem to work. However, the self-extracting one does fine (run wine first from the command line to get it to extract itself).
o Sometimes, the menu disappears. Resizing the window, even if just slightly, makes it reappear.
Other than those, I've made many a DVD from the files that TMPGEnc under Crossover uses.