I have both an iPad (1st Gen) and an iPhone 4. I sync both of these with iTunes on my iMac. I end up getting apps on my iPad that I really only want on my iPhone. Is there a setting I can configure to have sync work like I want?

Once each device is connected to iTunes, go to the apps tab on the device and tick the apps you want and untick the ones you don't. You can also organise where they appear and in folders if you wish, sometimes easier than doing it on the device itself.

You could also just use 2 iTunes libraries. Thats what I do with my iPad and nano.

I find two libraries as a bit of a chore, different playlists from the same library is the way I do it, no problem if you sync to the wrong library then because you forgot to switch before syncing.

Originally Posted by DefBref

I find two libraries as a bit of a chore, different playlists from the same library is the way I do it, no problem if you sync to the wrong library then because you forgot to switch before syncing.

It does get confusing.

I think the option you are looking for is at the bottom of the Apps list on the Apps tab for each device. This states "Automatically sync new apps". It is probably ticked in your case.
That's why when you sync a new app from your first device it ends up on your second.

Hope that helps.

Thanks for the help everyone. I got it all sorted out today thanks to these tips.

Great to hear you got it sorted.