Hi,
I don’t usually recommend a lot of web based tools but I had to mention this one, sitecheck.sucuri.net. This quick little web based malware/site scanner just saved me about 2 weeks worth of work by locating a segment of .js that was causing a malware warning to be thrown only in certain browsers and anti-virus scanners.
Because the .js was new and buried about 9 layers deep in a wordpress plugin, it would have been nearlly impossible to locate by hand. This tool pulled it up in about 30 seconds. Well done sir web scanner…