I've completed a very rough draft of a complete sane merged-mining implementation for Eligius. By sane, I mean it adds no potential harm to the Bitcoin mining operation. This goal is accomplished by making minimal changes (only 2 simple small patches) to bitcoind, and having it ignore problems with the merged mining manager.
The code is all MIT licensed for anyone to use, but I am posting it primarily for new developers who want to prove their skills and get involved more with bitcoin development. Parts 2 and 3 of this implementation are functional, but incomplete. They need some cleanup before they can be merged to mainline codebases (bitcoind and merged-mine-proxy). I'm available on IRC if anyone tackling this needs mentoring/assistance.
It is made up of 3 parts:
1. Coinbaser -- relatively simply branch/patch for Bitcoind to allow mutations to the coinbase transaction; it wasn't merged to 0.5, but ready to go as soon as 0.5 final is released (as a feature in 0.6); stable and well-tested
2. "gotwork" outbound
JSON-RPC call -- very simple patch for bitcoind to make an outbound "gotwork" JSON-RPC call whenever a work is submitted; needs cleanup, but otherwise works; there is a single hash/dictionary parameter with "hash", "header", and "coinbaseMrkl" keys
3. Hacks to merged-mine-proxy to run parallel to bitcoind -- this hack only supports a single aux chain, and will need its own merkle root maker to support more; it needs cleanup to be made compatible with the current merged-mine-proxy usage