There's a number of free and a few purchased iPhone apps that were downloaded to an iPod Touch in the last couple of years, none of which will show up in a new Windows installation of iTunes. The goal of them showing up on a computer is the ability to delete many of them no longer used.
Here's a sequence of actions in an effort to get them to show up on a new Windows iTunes 11.01.12 installaton:
1) Purchase of an iPad, where all the purchased past store apps display correctly under the "Purchased" tab
2) Installed the latest iTunes on a Windows 8 computer in order to display, then delete all unwanted app store "purchases," whether free or paid.
3) Had five defunct authorized past installs of iTunes which needed to be wiped out in order to authorize a new install. Did that.
4) Successfully authorized the new Windows installation of iTunes 11.01.12 with one and only ID ever made, and it shows that, as well as the new iPad as both authorized with the same ID.
5) Under the "Preferences" menu, then Store and Advanced, checked Apps under Automatic Downloads. Always check for available downloads and Download pre-orders when available are also checked.
6) Went to Store menu item, then chose "Check for available downloads" from there. No legacy apps are available and it says: "All purchases have been downloaded for this Apple ID."
The result of all this is that there's still about 30 apps that had been downloaded for an iPod Touch device which don't display in the Windows iTunes installation and thus are still not available for removal.
iPad mini Wi-Fi, iOS 6.0.2, Windows 8 Desktop with iTunes