Computer reset to default-like state, missing files.

I was working late on an assignment, and once i was complete, i saved, and shut my computer down, just like every other time that i used my iMac. The next day, my computer started up normally, i logged into my account, and i found myself puzzling over why my dock was reset, the two stacks "Documents" and "Downloads" were silver question marks, my hard drive icon was missing (fixed that in finder preferences) and everything on my desktop was gone. Unlike the HD icon that i could make reappear, these files were GONE. I searched my entire HD and couldn't find a trace of them. I also noticed that all of my applications had been reset. When i opened iTunes, it went through setup assistant, but thankfully my music was still there, along with my photos in my iPhoto library. All of my applications still had all of the data, but they were acting like i hadn't used them before.
After doing some research, I have found that the cause may be the name of my home folder being accidentally reset. Unfortunately, this isn't true, because my home folder has exactly the same name, and haven't even touched my home folder.
If you can find any way to help my computer return to the way I had it at, and help me find those missing files, It will be deeply appreciated.

So running +Repair Disk+ did not report any errors, or did it report errors that were then repaired successfully?
If it did report errors that were repaired, the files may still be missing after the repair. The actual data may still be on the drive, it's just that the file system has lost track of those files. You may be able to use a data recovery program to recovery that data. However, if new data has been written over the disk space used by the lost data, that portion will not be recoverable. One such program is
http://www.prosofteng.com/products/data_rescue.php?PHPSESSID=216be88cbbb8a850c5f 0b9decfb1dac4
The multi-functional TechTool Pro (Micromat) also has a data recovery tool.
If it did report errors, and they were NOT repaired successfully by Disk Utility, you may be able to use a third-party utility such as TechTool Pro or DiskWarrior (Alsoft) to do the repair. They may be able to reconstruct your disk directory data so that some or all of your lost data is recovered.
If NO ERRORS were reported by Disk Utility, the cause of this problem may be user-related. Is it possible you mistakenly moved the files/folders to a new location? For example, if you accidentally dragged the Library folder (the one in your user home folder) to a different location, since the user and application preference files are in there, your apps may run using the default settings the next time you run them. The Dock would also get reset. Use Spotlight to search for one of your missing documents, by file name. If you actually find the path to one such document, you may find them all along the same path. If they were accidentally sent to the Trash, but you have not emptied the Trash, they may be in the Trash.

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