UPDATE: HA! So I was *so* close to the real thing! Turns out that instead of 240 Nintendo DS Lites, they used 200 clustered Sony PS III's! I actually guessed that in an email to Sotirov, too! I can't believe you people doubted me!
I initially thought they used the go-kart crashes in Super Mario brothers to emulate MD5 "collisions."
Check out Ryan Naraine's write-up here.
So Alexander Sotirov and Jacob Applebaum are giving a presentation tomorrow at 25C3 titled "Making the Theoretical Possible."