During my days working as an in-store PC tech at Circuit City, these were techniques I developed for cleaning heavily infected computers.
This is what I did if the client's computer won't boot, freezes during startup, or constantly crashes.
1. Remove hard drive and connect it to a clean, anti-virus protected computer.
a. Run a virus scan on infected drive
b. Physically delete known virus files/folders
c. Run a checkdsk to correct any file system errors, which was done though command prompt> chkdsk /r
2. Reinstall hard drive in client computer
a. Boot computer into safe mode
b. Used CCleaner & MSCONFIG to disable any viruses/malware from starting during boot
c. Run an antispyware program such as AdAware or Spysweeper (run portably through flash drive)
d. Scan for viruses with client's AV program, if present
3. Reboot client computer normally
a. Run CCLeaner to delete temporary files, cookies, etc
b. Defrag client's computer, I used Auslogics Disk Defragmenter (on flash drive)
c. Check for internet connectivity then update client's AV program, if it hadn't already.
d. Scan for viruses with client's AV program to ensure computer is cleaned

And if all failed, or the OS was damaged too much, then we reinstalled/recovered the OS