What is the best way to 'clean' my computer?

To add to the existing answers. Uninstall with Revo Uninstaller. This will find all files and registry entries associated with the uninstalled program. You choose which of these to actually delete. It will also automatically create a restore point, should you accidentally delete important files.

I also sometimes use WinDirStat. This will create an overview of all the files on your hard drive. It also gives a graphical representation of the used space. This is handy to find large files that are left behind (some iso for a VM, for example).

Do some scans for other malware (you only mention viruses). I use MalwareBytes and Spybot S&D.

If your boot is becoming slower, use Soluto. If you're an advanced user, you might be better off with Autoruns.

Also consider that your hardware itself might have become slower over time. Especially if you're using an SSD, wear can become noticeable in a relatively short time.

You might also want to try and find whether there's any software slowing your PC down. You're best off with Process Explorer for this. It shows all information about all the running processes. (seriously, it shows everything you would ever want to know about a process, and more)

If you often install and remove stuff, because you just want to try something out, System Restore is your friend (you can even give it some more gigabyte of space if you can spare, that is). Seriously, that thing really improved since XP. In Windows 7, I have installed a "Lion Theme", which I've seen in an article from Lifehacker. (I thought it's some good stuff, since Lifehacker featured it.)

Instead of something good, my PC couldn't boot up. After a force-reset, it took about 40 minutes to get to my desktop, and my desktop freeze after a few additional minutes. Anyway, I fired up the USB (with the Win 7 installer), and went right to the recovery section. I was surprised, but it restored everything. Correctly. Not a single trace of that crapware, no hassle.

For cleaning? You can find so many applications and questions about this even on this site. Just check the search bar with the keywords.

What can you do if you didn't restore? I know we are over with this stupid "monthly reinstall" thing, but I think you should really do a reinstall. Save your data, and go for it. (But do it the clever way. Save all your data, and write up what applications you used, had installed, and so on.) And next time, don't forget. There is a thing called, Virtualization, that might help. You can just put everything you want into a VMWare guest, and use snapshots. That way, your host OS is protected and safe. (Or VirtualPC, or VirtualBox.)