Go into var/mobile/applications and look in those folders. Inside, there should be a folder that ends in .app (ie. whistle.app). Open the one you want to edit, then open info.plist and edit the "CFBundleversion" and (if it exists) the "CFBundleShortVersionString" keys to a number equal to or higher than the latest version on the App store. Open the store and the badge should go away because it thinks you have the latest version.