By now most of you have probably accumulated a ton of apps, but you don't want every one of them to sync to your iPhone. You have it set up the way you want it now, but if you restore or sync a new device, iTunes will try to sync every app you have.
So the easiest solution is likely to deselect all of the apps you have an manually select the ones you want synced. To do this, go to the applications sync tab in iTunes and command-click (control-click on Windows) the checkbox next to an app. This will tell iTunes to uncheck every app, not just the individual app you clicked on. From there you can check the apps you want. It works in reverse too, but for this example we're assuming you don't want to select them all. Enjoy!
There are a lot of different suggested methods for reducing the sync time for the new iPhone software, ranging from re-installing apps to any number of things, but Scott Paterson with UKMac.Net has stumbled upon one he believes may have solved the issue for him.
TUAW's Erica Sadun raises a very interesting point with the way the new iPhone 2.0 software syncs with iTunes. Where with the old software it simply backed up documents and data for the most part, the addition of the App Store now causes it to back up all downloaded apps to iTunes every time it syncs as well, taking significantly longer to sync. This is especially true for graphics and sound-rich games, which are a lot of fun but take a long time to sync.