I mean things like hitting ctrl+y to bring up player controls etc. I've seen a few MMF made games that disable this, and have their own gamepad configuration options.
Wings of Vi actually had a lot of customisable application options but I've no idea how to handle things such as changing v-sync/controls in-application. Anyone know how this is done?
I think you can disable those things by just removing them from the application's menu (simply disabling the menu bar doesn't seem to do it). You can find this in the application's properties. It's in the second tab, about halfway down where it says "Menu Bar [Edit]"
I think once you start editing/removing the default menu options, they end up losing their default functionality, and I'm not sure if there's a way to get that back. So just be careful if you value that stuff at all.