Operating systems do routine maintenance in the background. Like defragmenting.
Just run your anti-virus. Some folks opt for an additional antimalware/spyware program too.
If you think your anti-virus needs to be double-checked, run a free web based anti-virus scan from a different brand anti-virus company.
As always don't visit bad websites, click bad banners, and don't download and run strange strange programs.
In worse cases, one can always re-install the OS from scratch after backing up the personal files. In the case of MS operating systems this tends to unclog them in any case if it hasn't been done in awhile and you've installed and uninstalled a ton of junk programs in the past.
For testing weird programs, create a virtual machine and run them in that. Sandboxie might work as well I suppose.
For secure storage you can use True Crypt too.