I just put these instructions in my BeyondTV post, but since it is universal to all applications that use hotkeys, I thought I would repeat the info:
* Using http://www.windows-spy.com/ or similar, find the "Class Name" and "Window Name" for the program you want to control. For BeyondTV, these were "Streamzap.WM.D3D" and "Beyond TV".
* Write down the shortcut keys (e.g. pause=space bar). Then look up the virtual key ID's on MSDN (e.g. space bar = 0x20 hex = 32 decimal).
* Create a "send message" event in XLobby:
Class Name = Streamzap.WM.D3D
Window Name = Beyond TV
Message = WM_KEYDOWN
wParam = 32
iParam = 0
* If you wanted to be really picky, you ought to send a WM_KEYDOWN, wait 100ms, then a WM_KEYUP to simulate a real key press. This is necessary if your app has a shift+key types of combination (e.g. for Alt+Enter, use this sequence: keydown Alt, keydown Enter, keyup Enter, keyup Alt).
* Click "Test" to test to see XLobby remote control your application!