VirtualDub is a well-respected Open Source video processing tool that currently only runs on Windows (or via WINE).
Having looked at the code, it wouldn't be impossible to port it to Unix; it uses some Win32-style inline assembler, but most of the rest of the code should be fine. It could be given a new native interface, or just use WINE to get the port off the ground.
Alternately, you could build an entirely new application with a similar interface, just borrowing code where necessary. This might be easier to get GStreamer codec support.