Hi
I work at Google helping webmasters. Hopefully there won't be a next time, but for reference, your best bet is to post in our forum specifically about this type of issue: http://www.google.com/support/forum/p/Webmasters/label?lid=2...
For your specific case, unfortunately it can be anything. Start at the HTML and JS and see if it's different in ways you don't expect. Check for obfuscation techniques like base64 encoded PHP code, or JS code in libraries that is not in the original distribution. It really can be anything. Also check your .htaccess, any CMS and its plugins, etc. Really check everything.
That should identify the issue. Once you do, fix it, and try to understand why it happened. Was your FTP password compromised? Was it a known vulnerability in your CMS? Was it a rogue plugin you installed by mistake? Identifying the attack vector is very important as you will need to close it too. Otherwise all your hard work fixing the site will be undone in no time.
Also be sure to check any other parts of your site: the attacker might have entered through one CMS (say a forum) and compromised another (say a blog).
That's basically a summary of what you need to be doing. We have a very detailed guide about dealing with hacked sites: http://www.google.com/support/webmasters/bin/answer.py?answe... . It recommends quarantining the site and returning HTTP 503. That's a very good first step.
And if you need more help, seriously, the forum I linked to above has a great community that knows a lot about identifying and fixing these issues.
Hope this helps,
Pierre