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I don't have links handy, but you can look up all of this stuff online. My general clean up order goes (every couple of months):
(1) Your anti-virus software (I use McAfee because it's free with Comcast. I run it more often than every two months but as part of my cleaning regimen I do it again).
(2) A-squared Free. Good at finding trojans and worms.
(3) Rootkit Revealer. It tells you all of the programs that have hidden themselves from Windows. It isn't an automatic tool though and after you find rootkits you need to look them up on thier forums to see if they are harmful.
(4) CCleaner.
(5) Page Defrag. I use this instead of the built-in Microsoft version.
(6) Contig. DOS prompt program that finds what Page Defrag doesn't.
I used to use Regcleaner but it doesn't like multi-core CPUs for some reason. Oh and I forgot, before I run these programs I like to backup my registry using Erunt. Every 6 months or so I use a program called DriveImage XML to backup my entire drive to my external one.
Everything I listed is free to use except for the Anti-Virus (which is free from Comcast though). If I switch to FIOS I might pick up Kaspersky or something like that, haven't decided yet.
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