ergophobe - 1:44 pm on Oct 30, 2012 (gmt 0)
You can use the Sucuri Site Check (http://sitecheck.sucuri.net) to find out what the various authorities are reporting.
From there, you need to start with some detective work. When you say you couldn't find anything, how did you go about that? I would download a default distro of Joomla or, even better if you have it, a known safe backup of the site, and run a diff to find out what's different.
While you're at it, check the whois data for both domains.