Check the User Account Control Settings. Is the bar set all the way up? I have mine set to the first setting: Notify me only when programs try to make changes to my computer (do not dim my desktop). Run a scan with Hitman Pro. Here's the link:
Downloads - SurfRight. It works great! It's a cloud scanner that uses sigs from multiple firms. It'll boot before windows to remove extra pescky malware. If you don't seem clean, use Superantispyware and Spybot.
And true. You never know if you're 100% clean. But most infections are low-key without any special technology. And sec firms are getting faster, better, and stronger, so you should be fine. However, if you have a BOOTkit, reformatting the drive may not help. You need to scrap the physical BIOS!