I really hate syncing my phone these days because whenever I do I have to wait for all the apps I've downloaded since last sync to transfer to the computer. I download a lot of apps so this process takes for ever. So: can I opt out of backing up my apps?
Yes. You can disable app syncing.
To do this:
- With your device connected to iTunes select the "Apps" tab.
- Under the app listing, deselect "Automatically sync new apps".
New apps will no longer sync with iTunes. They will still backup to iTunes or iCloud, however, so you have no need to fear losing them should your device information be lost.
Note: all instructions provided work for iTunes 11.
iTunes sucks. The only thing you can do is change the owner of the directory where the apps are stored to "root" and change the permissions. The apps are no longer copied, however it still takes time for iTunes to process all apps.
cd ~/Music/iTunes/iTunes\ Media sudo chown root Mobile\ Applications sudo chmod 0700 Mobile\ Applications
now iTunes no longer has access to the directory, so it cant copy the apps. You might get a warning, but you can ignore this.