It is important to note that Square-Enix has absolutely no method of retrieving a stolen account, while almost all other MMO's have some methods in place. Thus anyone who lost an account due to this hack is completely screwed at the moment.
Also worth mentioning is that this is not the first time a fan site has been compromised resulting in hacked accounts. Several years ago, Allakhazam was infected with the fucksnow trojan.
Ironically, Allakhazam.com has a message from SE posted on its' front page regarding the recent hackings, but it's basically a "we know about it, and it sucks to be you" message.
http://ffxi.allakhazam.com/sdetail.html?story=11667Official statement from Square Enix:
We have received reports that a popular third-party FINAL FANTASY XI website had been infecting customers with malicious software. Our Legal team immediately contacted the hosting site of the offending third-party website and had the site taken down until the issue could be addressed. While the website main page has had the offending code removed, we strongly recommend that our community be careful when they visit any website concerning FINAL FANTASY XI that is not endorsed by Square Enix. While we have no control over these third-party websites, we urge that the community contact us immediately if any similar incidents arise in the future.
We also suggest that our customers read up on precautionary measures they can take to ensure the safety of their information online.
http://www.playonline.com/ff11us/polnews/news10343.shtml