Is EFF's proposed Sovereign Key system similar to how Namecoin/Bitcoin works? To avoid the problems caused by the current SSL certificate infrastructure, the Electronic Frontier Foundation has proposed Sovereign Keys, which appears to be backed by a distributed, append-only datastructure that can grow to hundreds of gigabytes. That sounds awfully familiar to a block chain. Are there similarities between Sovereign Key and Bitcoin (or Namecoin)? Do they employ a related approach or is this just a superficial similarity?
No.  Sovereign keys are simply a technical mechanism to use the DNSSEC trust anchors instead of companies like Verisign.  Trust is still centralized; it's just centralized in a different place.