First, let me say that LaunchBox is IMO the best thing to happen to the gaming/emulation scene in years!
Everything just works. No hassle, no complicated setups (given that your emulators/helpers are properly set up outside of LaunchBox), and a nice and clean interface.
Ok, so I've configured mine pretty much like everyone else, but I've also done a few things that I personally haven't seen anywhere else. For example, I added a "dummy" as the first entry for every emulator to remind me of the shortcut keys (mainly to exit). It's just an Image with only the platform associated with it (no program). I know that other methods exist, but it's nice to have a visual reminder when starting an emulated game. How many times have you launched an emulator game and asked yourself "what was that exit key again?" Aside from that I also make custom mappings (mainly to the Guide button) in Pinnacle game profiler for quick game/emulator shutdown.
I also have a custom section, which is used for Tools and Utilities. This is just a simple "Platform" used to launch apps like Game Profilers, Mod Managers and other gaming Clients like Steam, Origin and uPlay. Again, I realize that all this can be accomplished otherwise (especially the gaming clients as they launch with a game usually), but I really like this custom section I set up, as once again, it's more visual.
Best of all, it all works Flawlessly!!!