Turns out that a new snapshot (unofficial) version of my favourite DVD to iPod Converter is available. With the new version came new features like the one that allows me now to convert almost anything to wonderful iPod compatible movie files.
“HandBrake is an open-source, GPL-licensed, multiplatform, multithreaded DVD to MPEG-4 converter, available for MacOS X, Linux and Windows.”
I tried anything in my library, including some matroska movie files. Just everything worked – amazing!