I don't think your going to be able to do that. The iPhone (and iPods) can only be synced to one iTunes library at a time. While you are able to get around that if you want to sync Podcasts from one library, Apps from another, and Music from a third, you can't sync the same category from 2 different libraries.
That being said, the one thing I can think of that might work is if you check the box to manually move media onto your iPhone in both itunes libraries, you might be able to drag and drop apps from both onto your phone. Look on the bottom of the Summary tab next time you plug in your iPhone. Click the manual box and give it a try. Be sure to enable it on both you Windows and Mac partitions. I'm doubtful that this will work, however.