Good point, I have had apps pulled from the App Store that I was still interested in loading on our new iPhones/iPads. Week Cal HD for iPad (before iOS 5 broke it), iFitness/Full Fitness, VLC Player, etc.
Although being pulled or discontinued means these apps are no longer updated and eventually stop working 100% or become stale relative to the competition, motivating me to eventually find replacement apps...
Plus having gotten used to operating our iPhones/iPads independently of the computer thanks to iCloud/iOS 5, needing to sync back to iTunes on the computer just to add these pulled apps (to new or restored devices) feels like more of a hassle than before.
But anyways, my curated list of iOS apps on the computer grew beyond 100 GB (even after deleting the purchased apps I no longer want to keep), and my HDD ran out of space. I used to also maintain these apps on my family's other computers around the house which still have enough HDD space, but it just made their imaging backups that much bigger. And constantly updating the apps in iTunes was a real hassle (with thousands of apps there's always a lot that have updates everyday), since I was kinda OCD about updating...
So I gave up maintaining the computer copies of apps, although updating the apps on all our iPhones/iPads is still a hassle
I wish iOS 5 has automatic background app updates, and even better, delta/differential app updates to cut down on the time and bandwidth.