I went looking for a Cuttermaran equivalent for Ubuntu, for cutting the MPEG2 streams recorded in MythTV. First I tried GOPchop, but despite indexing the file, it didn’t show it in its file listing after opening it and so I couldn’t really do any editing with it.
Then I found Avidemux. Despite the unfortunately limited -sounding name and repository description I decided to try it and boy, am I glad I did. It’s quite capable of cutting MPEG files as well as dealing with many other codecs, so I highly recommend it. It’s even available for Windows.