Help with app sync in iTunes

This problem is affecting my iPad, iPhone, and iPod but I thought I'd post it here. I'm sure I'm overlooking something simple so please be patient with me.

My PC's hard drive crashed so I've rebuilt my computer and want to resync my devices with it. I plug them in and iTunes tells me they synced fine. When I go to the Apps section, the sync app check box is unchecked. If I select it, it says that it will replace all the apps on my device with the apps on my PC which doesn't have any apps on it. It seems that I tried checking it with my iPod and it jacked up all my folders and most of my apps (but not all) were removed.

How should I proceed? How do I make a back up of my devices in their current state on my PC so that I can sync Apps with it normally?

 

Anyone?

 

While that would work, it's a pain to do and without checking the sync apps button in iTunes, I loose the ability to easily re-arrange my icon layout in iTunes. There has got to be another way.