So, instead of giving up, or following the suggestions of "just turn off ur second monitorz whiel playng lol!", I have made a little app that will detect when the game window has focus and clip the cursor to its client area for you :). It works a treat, and you can easily add support for other games! Hooray!
Currently it supports Generals and Generals Zero Hour...and notepad (for testing). You can easily add support for new games by editting clipperdb.xml - you just need to know the game window's classname and title.
See readme.txt for details.