I have a similar problem as the OP. I installed Catorize and mymenu (in my attempts to get a proper menu configuration, although neither of them did what I wanted) and just today I uninstalled them, since they didn't' do what I was looking for.
My problem is that after I uninstalled them, my menu was only listing the default programs for my phone, not the ones I've installed. Searching for a solution, I found that ApMeFo program, I had to create a shortcut to my desktop (considering I can't see any of the installed programs in the menu), but it won't open (some programs seem to be opening and others don't).
I did what MohammadAG posted, to get the hildon.menu file to reset to defaults, but the menu is still the same. I have restarted the phone after I made the changes to hildon.menu too, and it didn't make a difference.
Is there anything else I can do?

EDIT: I installed Catorize again and it seemed to fix both the menu issue and my desktop shortcuts problem; I can't see why it would do that. I'm afraid of uninstalling it again and having to go through all the trouble I did before to do anything... (I couldn't get to the App Manager, since it didn't appear in the menu list; so I had to install a program from the Ovi Store and then work with the App Manager from there). Does anyone have any ideas why I get this problem?
I checked out the hildon.menu file before and after installing Catorize and it didn't seem to have changed the file at all.