I had that problem once.. I was mounting my /home as a partition.
I allocated free space to that partition but it wasn't used, so told it to consider it a mount. It did that, copied everything, and when I rebooted everything was... missing!
That was because I didn't have my data in my home directory, and I forgot to MOUNT the filesystem after setting it as a mount point...
Soo, You problably deleted the application listings..
Not exactly sure if you will have to add everything back manually or not, but heres an idea:
Right click on the taskbar panel, go to Add to Panel, and select "Main Menu", and it has a foot next to it... It might add the menu back to how it was, or just add the same thing you have already