Lost all my apps after I did a system restore on my replacement I phone 4

Hi, I got my I phone stolen and got a replacement phone, I did a system restore and everything came over except for all my apps.  What can I do?  Yes I did back up my phone prior to it being stolen.  I did remember seeing all my apps on my itunes at one point.
Does this happen when you try to connect a new iphone with old itunes account?
I might of downloaded a new firm ware for i tunes before I did a system restore on my new iphone 4, could that of triggered my apps being missing?
please help, I have over 100 apps that I don't want to loose.  thanks for anyone that knows whats going on...

If your apps were in itunes on your computer, then they should still be there.  Just sync them back to the iphone.
BTW, the backup that itunes performs when syncing does NOT include music/apps/movies/tv shows etc.
Anything purchased on the iphone would have to be transferred to your computer.  File>Transfer Purchases
Unlike music/vids/etc, you can redownload apps
How to redownload purchased apps from the App Store

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