UberMQ is a clean-room implementation of the JMS 1.1 API (topics and queues), based on Java NIO for speed and scalability. It supports TCP, SSL and LRMP multicast connectivity, and is highly pluggable so you can customize various aspects to your needs.
Naanou is a 'clean-room' implementation of the published Chord protocol from MIT. It is a completely distributed hashtable P2P network, with provable high-performance characteristics.