Restart their router :^)

de-centralize.

Install http://wiki.debian.org/iptables

They could use a hosting provider that has DDoS protection, such as OVH. OVH guarantee to mitigate all DDoS attacks no matter what size or duration. I've been using them, and their DDoS protection works really well.

Or, if they prefer to host themselves, they can spend the money to buy the bandwidth and Arbor (or other?) equipment.

The fact is that -- like github -- they are being DDoSed and have to do something about it if they want to stay in business. I'd be interested in hearing what github did to mitigate their attacks. I can't find any info on it (but I'm guessing that perhaps they want to keep it secret).