You can always try playing with 'fake' window messages. I once coded a program that tricked a paint application on a website (an oekaki board) to think the user was drawing an image, pixel-per-pixel, by sending thousands of 'fake clicks' to it's HWND.
All I had to do was find the target window using FindWindow(), and then use SendMessage() with WM_LBUTTONDOWN/WM_LBUTTONUP to make it think the user was clicking.
There is a pretty simple way to send a message to all opened windows (excluding their children) in the OS, it's called message broadcasting. For example, by specifying HWND_BROADCAST in SendMessage() all top-level windows receive the message.
Intercepting the stylus should be a bit harder. I haven't ever tried this, but there may be a way to use subclassing for that. If there was an OS-driven window that receives the input and broadcasts it to all other windows, you theorically could subclass it and voila, get control over what the PDA receives from the stylus.
Check MSDN for further information about that. But remember to be careful in playing with such a primary thing like stylus input.
Oh, and if you want a handy tool for some training and testing of how the windows react to window messages, you can use this utility I once wrote:
http://justt.cellosoft.com/files/PostMsg.exe
This is a PC build, but I can give you it's source so you can port it to PPCs, if you're interested.
I hope this helps :)
