As google has detected malware on your site, my first though would be have you tried Google webmaster tools
I havnt used them myself, but they may help you locate the source of malware.
It would also be worth your while to run RootKit Hunter
it can be downloaded from the download link on that page.
Unfortutly their are no tools available for use on a server that allows remote analysis of the machine in the same way that can be done using HJT (and other tools) for locating and removing malware from windows machines.
First change your usernames and passwords, if you site has been hacked these will be known to the hackers.
The best way to find malware on a server is to manually check each directory and file for malware. Start by looking for any file names you dont recoginse. Also take a carefull look at all the readme files, malware is oftern hidden in files named readme, knowing full well thats the one file most people dont bother reading helps them avoid detection!!
Once you have found and removed all the malware, again change your username and passwords. Its best pratice to change these every month if you can.
An alternative approach, assuming you have uptodate backups of your site. Would be to delete everything on the server, and then reinstall all the software you are using from fresh downloads, and then installing your own data from your backups. If you do take this approach, please check each back up for the existance of anything malicious before you install it.
If you are totaly stuck, we do have our own server support site, however the only way we would be able to assist you, is you would have to allow us full root access to your site, which quiet understandably you may not want to do.
If you are intrestesed in us taking a look at the server for you, please respond in this message, i will then send you a PM with instructions on how to join our server support site.
MWR Server Admin