I've created this little app because I wanted to run several different mods without messing up my folders: windows requires that all files be in the same folder so you can drag and drop them all together, and it's specially annoying on linux distributions if you don't have a file manager with drag-n-drop support.
Anyway, this is just a beta, so it may have some bugs - but it seems to be running seamlessly, so far. It supports "presets", which are nothing more than a bunch of wads grouped under a config to be launched together. You can also choose a neat pic for your preset.
You can set up the executable path of several engines and choose which one one to use in the main window. This app does nothing besides running the selected wads with the chosen engine.
You also can run a single wad directly - WITHOUT having to create a preset for it beforehand.
Cross platform - coded with Java.

Edit:
AvocaDOOM blog: http://avocadoom-launcher.blogspot.com.br/
Google Code project (svn and stuff): https://code.google.com/p/avocadoom/