Well I bit the bullet and finally updated to iTunes 11 yesterday.
Downloaded the full installer package and installed it. I did not
do the software update method. I then rebooted (in the past,
found some things didn't always work until a reboot).
Started up the new iTunes 11. After fumbling around with the
new interface for a bit and trying to get things back to semi usable,
I held my breathe and plugged in my iPhone 4S.
The result, everything synced just as it did before. Apps I updated or
purchased on the iPhone were synced just fine to my computer. Just to
make sure, openned up the iTunes folder and in iTunes Media-> Mobile
Applications the apps there were the same version as those on my iPhone.
Now, my install was with the 11.0.1 update, if that means anything.
Also, not sure if the full install approach made a difference versus
the update approach made a difference.
BTW, system was 2011 MacMini Server with Mountain Lion (10.8.2)
and iOS 6 on my iPhone.
One thing that did happen, I did lose artwork on several of my CD
rips that I had previously added manually. It seems if the album/CD
doesn't exist in the iTunes Store, it erases the artwork.