Yeah, I used to use Spybot S&D. I liked it, but yeah, Tea Timer got to be somewhat annoying. Like you say, it throws up an alert everytime something in the Registry changes. Great idea from a malware-protection standpoint, but it gets tiresome 'cuz so many legit things modify the Registry too (Windows Updates, security program updates, and, of course, pretty much any new software you install). And if whatever you're installing makes multiple Registry changes, you get multiple alerts. Sometimes you sit there and click "Allow" a half dozen times or more during the installation process.
What I found myself wanting to do was turn it off before installing anything, then turn it back on. But I couldn't figure out a way to do it. I think you have to uninstall the whole program, then re-install it without selecting Tea Timer as part of the package. About the time I was going to do that, I switched over to a new anti-spyware program (two actually). That was about a year ago though, so I dunno if this is still the case.
If you don't mind all the alerts, I think it's a great idea. Judging by how often it threw alerts up at me, my impression is that it's quite effective too. 😛