I figured out that there's only one thing keeping MPEG4 Modifier 1.4.3 from running on Mono, it's the "Shown" event added in WinForms 2.0. I worked around this and made a compile that runs mostly fine in Mono. Screenshot of MPEG4 Modifier 1.4.3 running on Mono 1.2 in Ubuntu:
Opening a file via the file dialog didn't work so well, it seems the file type filtering is broken and it doesn't show any files at all, but you can navigate to the folder and type in the filename manually. Or don't use the file dialog at all, just drag your file onto the "AVI Source" textbox.
It's
here if anyone wants to try it.
EDIT: Compiled a new version, increased the size of some controls to fix the text being cut off.
EDIT2: I think the file dialog issue is fixed in Mono SVN as of 2006-11-17, the file dialog filtering should be fine in the next Mono release.