Opening a new iTunes window for my apps (Windows 7) I've currently got around 700 apps installed on my desktop PC, and 500 installed on my iPad. 

I'm trying to remove all of the apps from my iTunes library that aren't on my PC, but it seems the only way of doing this is to delete my entire library and sync them back across which I have to be honest and say I'm not very keen on. It's a nightmare to have to keep clicking between them, especially in the new iTunes. At the moment I'm taking a screenshot every time I delete an app, which is far from ideal.

I'm wondering if there is a way to have one window open with a list of apps, and one window open with a list of my syncs within iTunes?
Certainly, deleting your iTunes library on your computer, then just syncing your iPad back to your computer would be the most ideal solution. There is no way to access old versions of iTunes when things weren't synced as they are now so the way you described isn't possible. However, as long as you have all of your stuff from your computer, then deleting everything there and just keeping the stuff from your iPad is probably the best solution. Sorry if it's not what you wanted to hear.