The new Bitcoin Foundation has issued a year end address where they have highlighted the work accomplished so far to produce a higher quality reference Bitcoin implementation. The foundation which came together in late October has focused their efforts on producing a patch set for the Bitcoin 0.5.3 codebase that results in a minimal reference implementation of the Bitcoin Protocol.
Among other thing their patch set manages to remove cruft like the historical checkpoints, the legacy alert system, upnp, and MinGW hooks used for Windows builds. The process hasn't been painless with a wedge block at height 252450 requiring patched settings for the Berkeley Database which handles the blockchain, and memory leaks and general instability plague initial synchronization. The foundation plans to focus on wrestling with the synchronization issue and thoroughly testing any fix for regression issues that could break compatibility with the network.
The progress made so far gives reason to hope that the foundation's goal of offering a better reference implementation of the Bitcoin protocol might not be far off in the future.