While it was not the cause of today's drop[1], that is a big part of the problem. While they are frantically working on decoupling their website from the trading engine, they are still connected, and DDoS attacks are still effective at causing extreme trading lag.[2] Such attacks have been the root cause of several mini-panics over the past couple weeks.[3]

Of course this is bad design, but you have to remember that this website started out as Magic the Gathering Online eXchange. It was built to trade playing cards, not to serve as a multi-million dollar currency exchange. The trading engine was retrofitted for bitcoin, and was stuck with several bad design decisions as a result. While I agree this should have been fixed long ago, MtGox has had its hands full recently. The massive growth in its userbase, the ever-growing verification queue, and the fact that it is expected to be online 24/7 have made things difficult.

However, I suspect the main cause of today's massive has to do with this: https://mtgox.com/press_release_20130409.html

It will interesting to see what effect this policy change will have.

[1] https://www.facebook.com/MtGox/posts/455962117821534

[2] https://www.facebook.com/MtGox/posts/453409538076792

[3] https://twitter.com/MagicalTux/status/320043013420249088

It's unclear, but it seems in any case the separation is weak

http://www.facebook.com/MtGox/posts/453409538076792

"There are a few things that we can implement to help fight the attacks, such as disconnecting the trade engine backend from the Internet. By separating the data center from the Mt.Gox website, we will continue to be able to trade"