To simplify, you either have a problem with the hardware, a problem with the software, or both.
Figure out if your computer has boot from CD or boot from USB enabled, and the steps to boot from external media if it's disabled by default. A quick Google search often speeds this process along.
Use a live cd like the Ultimate Boot CD to check the RAM and hard drive for errors. Test the RAM with Memtest86+, and use your hard drive manufacturer's test suite, such as DLG for WD hard drives. This will rule out most problems with memory and hard drive issues. You could also check system temperatures if you wanted to rule out thermal issues.
Next, run a Linux live CD or boot a Linux distribution from USB. If this exhibits no problems and runs much faster than the installed system without any stability issues, it's boot and nuke time. Transfer any "can't lose" items from the hard drive to some sort of external media at this point. You'll want to scan these files for malware before you get them anywhere near a clean PC. It's preferable to scan these in some sort of live environment.
If you hadn't already tried the restore partition, you could choose to perform a "destructive restore" from here, but I don't have a lot of faith in restore partitions, as they can be infected by malware just like the normal partitions. This is where being a Linux user is nice, because you don't have to sweat about license keys and install media.
If your mind is set with staying in Windows, here are your steps:
Locate a system restore disc or a legitimate version of the operating system that you wish to install. Verify that it is a "full" version, and is not an "upgrade" version that requires a previous version of the OS present in order to install. Make sure you have the license key and input it correctly. Be prepared to call the manufacturer if the restore doesn't work right, or Microsoft if the OS install goes wrong.
Take the previously mentioned "Ultimate Boot CD" and run Darik's Boot and Nuke. It will take a while to erase the drive. Since you plan on reinstalling, you can use one of the quicker format modes. A "quick erase" or "DoD short" should do the trick.
Install the operating system from scratch on the (now blank) hard drive.
If necessary, transfer the old files that have been scanned multiple times for viruses back to the fresh operating system install. Enjoy the process of installing software and system updates.
Curse yourself for not having a more recent backup or implementing a system image backup routine. Vow to be better at it, and hope that there won't be a next time. There probably WILL be a next time.
After typing into the start menu, you need to wait for items to appear. I've experienced that before. The delay you see with, say, cmd is the app itself lauching – Cole Johnson – 2012-11-26T23:26:42.123
5I had this happen on a family member's laptop recently. Once I was able to get into it I scheduled a chkdsk, which would not complete after three attempts, reporting that the disk was so messed up it couldn't fix anything. The disk is getting replaced, and I'm going to mount it on a USB to SATA device to see if I can pull any files from it. This may not be related to your issue, but it wouldn't hurt to "check." – Bratch – 2012-11-27T00:55:17.030
1http://security.stackexchange.com/questions/24195/how-do-you-explain-the-necessity-of-nuke-it-from-orbit-to-management-and-users – Boris Treukhov – 2012-11-27T12:06:26.293
29"Nuke the site from orbit, it's the only way to be sure." - As in all cases of serious malware infection I would suggest to salvage the data you can using a Linux live disc and then reinstalling Windows. Otherwise there is a fair chance that you will not clear very bit of malware and will either have to restart fixing it later OR (and potentially devastating) someone will keep using the machine under the assumption that it is clean although it is not. – fgysin reinstate Monica – 2012-11-27T15:54:08.127
Just use the Live-CD to copy your data on an external driver and re-install the OS. – xavierm02 – 2012-11-27T16:24:09.097
@fgysin recovering arbitrary data from an infected computer and nuking from orbit are mutually incompatible activities because data files can carry an infection to the new computer (ex office macro viruses); even if, in the far too common case, where the user doesn't have a recent backup to restore from it's the closest you can come without massive protest. – Dan is Fiddling by Firelight – 2012-11-27T22:11:04.173
I had to clean up a system infected by ransomware. It had a similar disk performance problem that was caused by the trojan scanning the disk looking for all files/folders and setting the hidden attribute. Do a google search for 'optimizer pro removal' good luck – jqa – 2012-11-28T02:02:11.677
If it's not malware, here's betting there's an issue with the graphics card. – James P. – 2012-11-28T06:34:19.760
If it not the malware slowing things down, check the dust levels in the case. I fixed the speed problems with a computer once by cleaning out the dust. The machine was overheating because of it. – Darryl Braaten – 2012-11-28T15:03:51.667
2try
format c:/
– Phillip Schmidt – 2012-11-28T19:50:11.070