Joining webm videos under Linux

As Lou mentioned, try mkvmerge like this (from command line):

mkvmerge -o output.webm -w file1.webm + file2.webm

Remember that the WebM container format is a strict subset of Matroska, so Matroska tools will work on WebM files. Try mkvmerge (which ships with mkvtoolnix) to re-mux files without re-encoding. The result may or may not be satisfactory for your purposes, but mkvtoolnix is mature and GPLv2-licensed, and well worth a try. There's even a mkvmerge GUI.