mkvtoolnix-gui(1) is a Qt(tm) based GUI for mkvmerge(1) (and will evolve to cover mkvinfo(1) and mkvextract(1) as well). It offers easy access to most of mkvmerge(1)'s options. All settings (e.g. source files, track options etc) can be saved and restored.
mkvtoolnix-gui(1) knows few options. At the moment it only supports a single file name. If that file name's extenion is '.mtxcfg' then it will be treated as a settings file and mkvtoolnix-gui(1) will load its setting when it starts. Otherwise the name is interpreted as being the name of an input file which will be added.
The latest version can always be found at the MKVToolNix homepage.