If you are getting a 0KB file:

Your source file may have the audio stream (#0.0) mapped before the video stream (#0.1). This is reverse from what the ffmpeg engine expects. You may fix this "Codec type mismatch for mapping"-error by indicating that the streams are reversed. To do so, check the "Invert mapping" checkbox in the audio tab.

If the video skips, is choppy, or pixelated:

Try upping the bitrate. You can push it as high as you like to get better quality video, as long as the resulting file you upload is smaller than 48MB.

If your original file type gets an error, such as an 'unrecognized' error:

You may be using a codec that is not supported by ffmpegX. A more common unsupported codec is the DV codec for .mov (Quicktime) files that are exported directly from Final Cut. If you use Compressor or another program to make this file into a more standard .mov codec first, this should solve the problem.

Other problems:

The Log may hold clues to why a conversion failed. You may access
the Log by clicking the blue "i" in the ffmpegX Progress window.