Hi guys.
I think RootAlyzer is a great tool - I myself have only just heard about Rootkits and how dangerous they are.

But to quote PepiMK from the thread mentioned above:

Spybot-S&D usually detects threats in our database only; RootAlyzer just shows any things it identified as hidden, without relating them to known malware. So you could use RootAlyzer to detect even rootkits that are not known yet; but one of the new plugins for Spybot-S&D includes kind of a rootkit heuristics (which is not as generic though).

In summary: use RootAlyzer if Spybot-S&D hasn't found the culprit and you're suspecting an unlisted malware.

Great job, Spybot team!