Spybot Search & Destroy is an application that has been around for the better part of a decade. In Bright Hub's most recent review, it came out with good marks for picking up spyware, although it should never be your only defense. Use the Advanced tab to set scans up automatically.
It does have some issues. When running it as a user, not an administrator, it will constantly tell you that you do not have privileges to have it scan everything, but when inside the program it does not give you the opportunity to run as administrator. This frustrated me a number of times, because I had it set to scan automatically when I started my computer. Eventually I stopped it running automatically, and instead started it on demand as administrator - which means I do not always remember to run it.
Because it does not scan for viruses, you do need to keep anti-virus software running. It, unlike a number of other anti-malware programs, does not interact badly with other security programs, so you can run an anti-virus program such as the free version of Avast.