Someone should build good support for merged mining into free open source pool software.
So far the easiest way to merged mine is to use p2pool, which was intended and designed for each miner to run individually as a node of a distributed pool, even though eventually people's determination to use centralised pools ended up being slightly / token-ly catered to by p2pool adding support for allowing third parties to use your copy of is, sharing out the coins of the primary chain.
Maybe though if merged mining does become popular it will give people incentive to run their own p2pool...
-MarkM-