Having recently migrated from an old machine to a new desktop, I had almost everything setup just the way I like it. Only, I couldn’t figure out how to transfer all the (free, haven’t paid for a single one yet!) apps from my iPod touch (2G) to the new iTunes install.
The default syncing that happens when you first plug-in the iPod didn’t work. When I tried to sync just the applications, iTunes politely threatened to erase and replace all the apps on the iPod touch with the non-existent ones on my computer. A quick search of Apple’s support site turned up the answer: File > Transfer Purchases from iPod. Alternatively, you can right-click on iPod in the iTunes Device list and select “Transfer Purchases” to achieve the same result.
The “reverse” transfer works for apps and other files purchased from the iTunes Store to any computer (up to 5) that is authorized for your iTunes Store account. Oh, and all of this (obviously) applies to iPhones as well.