Assuming you don't work with profiles, there's a folder Start Menu in the Windows Folder. It might contain a few shortcuts (you see in the upper part of the first column of the Start Menu) and it surely contains a folder Programs, which should contain the folders and shortcuts you don't see now. That's the go and search part (use Explorer). If there's no such Programs folder, make one?
With right click on taskbar, properties you can manage the folders and programs in Start/Programs. You might have to redo everything.
If the 'only' problem is that the folder accidentally got deleted, you'll be able to repair this more or less. In principle, it could be a symptom of another problem (viruses, hard disk problem). Let's hope that's not the case.
I am using Windows 98SE. When I log on my desktop appears correctly. When I click on START the Start Up Menu appears correctly. When I click on Programs nothing appears. The programs themselves have not been deleted since I can load them from icons on the desktop or from Windows Explorer. I must have inadvertently deleted or changed something which just removed the list since this happened suddenly. Will be glad of any suggestion as to how to get it back.