Try
this, Hitman Pro installs a bunch of programs (legal certified versions mostly, trail versions of others) and uses an automated script to run all of them. Catch is that you can't use your computer while it's running because it needs control over your mouse to work proper. The whole process takes around an hour and a half to two hours to complete, depending on the level of fucked upness of the computer.
After your done with that, run a virus scan if you have one (if not Hitman Pro comes with a trail version of one, be sure to turn that off if you have your own by the way). Can take an hour or two depending on the size of your discs.
And after that do a defragmentation of all your discs. You'll find that in your start menu under 'accessories' and then system maintainance. This also will take an hour or two if not longer, again depending on the size and fuckedupness of your discs.
To run the entire thing you'll probably need an entire afternoon. Luckily you only have to turn the last two on and let them go. In case of Hitman Pro I'd recommend checking up on it every once in a while to see if it's still busy.
Hope thats enough info for ya. Good luck.