Too many to list, but DO NOT use a registry cleaner/optimizer or whatever they want to call it today. They can cause much more harm than good.
For cleaning, it depends on what you need to clean. If it's viruses, then you need a good antivirus program (Free versions of Avast or Avira are fine) and a good antimalware program like Malwarebytes or Superantispyware. I prefer Malwarebytes.
For general cleaning, start by right clicking on your hard drive under My Computer and selecting Properties. Click on Disk Cleanup. CCleaner is also good for cleanup, but DO NOT use it's registry cleaner. It has also been known to cause problems in Firefox, so, if you are using FF, uncheck the options to clean it.
Organizing is up to you. Take some time, create some folders and start organizing your files. Organizing is really such a personal thing that I wouldn't trust a program to put things where they would make sense to me.
A forum community dedicated to tech experts and enthusiasts. Come join the discussion about articles, computer security, Mac, Microsoft, Linux, hardware, networking, gaming, reviews, accessories, and more!