What does the number mean next to Applications in iTunes? I have had "3" there for a long time. Little Number in a circle to the right of Applications in the Folder list.
I think it means you have updates pending. Go down to the bottom right of the window and click the "check for updates" button. It should show you what needs to be updated, and ask if you want to download the updates for all the apps.
The number is indeed the updates you have pending. I posted something about this a few days ago on my blog. I've had a 6 next to mine since the 2.0.1 update. I know all my apps are up to date but it says I have some available anyways. The versions of the "updates" it wants me to get are also much lower than the versions I already have