There are tools like rootkitrevealer (don'task me for the URL..I am too lazy)..
or useing the good old tools like HJT and Stinger on a BART PE os disk.. in other words a "remote" scan of the HDD.. that is where it isn't your os that is checking the registry and files..
For information on the BART PE disk setup have a look at IronGeeks tutorial on the subject