I like using folders of shrotcuts. They are universal. LiteStep, BlackBox, SPU (ShortPopUp), and other launchers can read them as is. Even the quicklaunch can do it. It is a native GUI, I find.
I actually started collect single function executables to add functionality to the such menus. Empty the recycle bin, open/close cd drawer, show/hide extentions, shutdown the compter... etc. You can do a lot when you look around.
I took SPU to a new level in auto configuration though. It has a variety of configurations that you set as parameters. It got very extensive, so the author let you put them in a file (loadable by a parameter, heh). I figured out a way to associate that file to the app. Put the file in a folder, put a shortcut to it in a launcher, and instant menu.
I also recomend hue recoloring. It makes a skin seem much more comeplete.
A comment on LiteStep: ya that is handy. It was added with OTS 1 (open theme standard 1). It had all the most common used apps listed. This made it possible to create custom luanchers that most ppl would find useful. Something like that is one way to go with the app, and it could easily read that part of OTS2 (it got updated) automatically. I recomend a readable, configurable text file one way or another, so it can be edited by hand if need be.
---This app may not need this though. LiteStep is so free-from, this was a solution to conform the chaos. This app, being a single purpose luncher, shouldn't really need it. Still, itcould be useful.