OK, as the question is about "tools" I will leave out day to day applications that I mentioned earlier.
I will also assume that we have an already built machine that has or did have a functional operating system, which I will also assume is Windows (as it is the most common).
INSTALLATION/REINSTALLATION
1. DBAN (Darik's Boot & Nuke) or Eraser
2. HDD Manufacturer's Diagnostics (eg. WD Data Lifeguard)
3. CCleaner
4. Auslogics Disk Defrag or Diskeeper Lite
5. Auslogics Registry Defrag
6. nLite/vLite
7. ImgBurn
8. Secunia PSI
SYSTEM CLEANING
1. CCleaner
2. Ad-Aware
3. A-Squared
4. Eraser
5. ExeHound
6. PC Inspector task manager
7. Spybot S&D
8. Avg/Antivir
9. Online scanners (eg Panda)
10. HijackThis!
11. Bionic CPU Peeker
12. Microsoft Malicious Software Removal Tool
13. WinPatrol
14. Disk Investigator
15. Blacklight
16. Combofix
17. Ultimate Boot CD
18. Disk Heal
DATA RECOVERY
1. PC Inspector File Recovery
2. PC Inspector Smart Recovery
3. Recuva
4. Undelete Plus
5. Roadkil's Unstoppable Copier
6. Disk Investigator
7. Ultimate Boot CD
SYSTEM INFORMATION & OTHER TOOLS
1. SiSoft SANDRA
2. Belarc Advisor
3. Auslogics System Information
4. Fresh Diagnose
5. RAMpage
MISCELLANEOUS RESOURCES
http://www.2-spyware.com/corrupt-anti-spyware
http://www.spywarewarrior.com/rogue_anti-spyware.htm
http://virusscan.jotti.org/
http://www.virustotal.com/
http://www.hijackthis.de/
Obviously there are many tools that perform similar functions, I have tried to restrict myself to those where you can get a copy that is free for private use.