I don't know about you, but those new longer iPhone syncs are just killing me. Once an App has been backed up, I don't see why Apple doesn't just back up the Documents and Library data rather than backing up entire applications every single time the iPhone connects.
What I've been doing is keeping just one or two apps on the iPhone at a time. That's fine for when you're developing and reviewing apps but it absolutely stinks when you want to carry the iPhone around and actually use your applications on demand. After all -- why bother buying them if you have to keep taking them off in order to save on sync time?
The worst offenders are the games. Full of yummy sound effects and graphics, they take up the most room during syncs and generally the software I least want to take off my iPhone.
You can disable automatic syncing for iPhones and iPods in the Preferences > Syncing settings pane in iTunes but it's an option with high risk, especially when updated data is important to you.
Here's hoping that Apple smartens up its backups and starts storing just changed data rather than every bit of every application.