stretching is an xbmc setting. Add AspectRatio to keymap.xml (see <FullScreenVideo> here for an example). It should work just like DVDPlayer (haven't tested). Shaders are still on my TODO list.
Each emulator actually has its own specific configuration. In the add-on manager, you can go to an emulator's info screen and hit "Configuration". Right now, the system directory is the only setting, and you don't need to worry about this - if an emulator requires a system directory, it'll automatically ask you for it on game launch. In the future, I'm adding support for the settings that show up in RetroArch.