I had the same problem with another website i own. After removing every iframe stuff, you need to change all your passwords. That won't help you too much if you don't scan your PC with an antivirus program and remove the trojan virus.

The real stuff that keeps away this infection is chmoding all index.php and index.html files with chmod444, this way the virus won't be able to write anything on your file. I tryed that and it really works. Give it a try and you'll thank me later, i assure you all! see more :)