I recently set up Windows Live Mail to read my Google Mail account, and I was periodically getting the "new mail" sound without getting any new mail. I discovered that Windows Live Mail was syncing the Spam folder and notifying me every time there was new spam. Oops. So I right-clicked on the Spam folder—subfolder of [Gmail]—highlighted "Synchronization Settings" and selected "Don't Synchronize".
I may have to do this with other folders as any new mail with multiple labels will show up in an IMAP folder for each label. I haven't noticed yet, but I'm guessing Windows Live Mail will then tell me there's a new message for each label it has.