|No guarantees that this is THE solution to your problem .. not enough information. Who, what , where, when is necessary - need the whole story.|
Start computer in safe mode, log in as administrator.
If the programs are not there, you have a major Windows problem. Disregard the
rest of this post.
If the programs are there, run antivirus application. Remove virus if found.
Create a new user. Shut down and log in as new user.
Your documents will be under the old user profile. Back them up, then Move them to the new user. If possible, once all data has been retrieved, delete the old user account.
Summary - it is possible to loose the current user part of the registry. Anything specific to that logged on account may be lost as well. You will keep whatever is common in all users, if this is the issue.
I have found this to happen on laptops that are left on, running excessively, etc.