I had many applications show up as "Installed" in the update pane of the Mac App Store even after I had updated them. Apparently, if you have copies of an application on your system, even on a secondary drive, they are discovered by the Mac App Store. This causes a problem if you have a copy an application in the /Applications directory as well as somewhere else on your drive. If you update the application in the /Applications directory but not the other instance then the Mac App store will display the application on the Update Pane, but list it as "installed". Simply deleting the other instance of the application will cause the Mac App Store to refresh it's data and remove the application from the update list.
[kirkmc adds: I was seeing that in the early days of Mountain Lion. After running the updates again, they disappeared; I didn't think to check my backup drive, were I clone my startup volume, to see if those copies of my apps got updated.
I just checked the Mac App Store and found two updates waiting for me. (I thought it was supposed to alert me when there were updates?) I updated one app, quit the Mac App Store, then re-launched it; that app was no longer listed. So this may be a transient problem that Apple has resolved, but I'm publishing it anyway, in case others still see this issue.]
Mac OS X Hints
http://hints.macworld.com/article.php?story=20120727110524438