Andrew Feenberg and I work on Marginalia, which is a reincarnation of an earlier open source online discussion software called TextWeaver (http://www.textweaver.org) we developed.
Derek mentioned Marginalia and the use of tags. It is true that annotation is not really a tagging function. We have always wanted to implement the tagging function, which we call it keywording, and it is still in the plan for Marginalia. I can see why Derek sees the smart copy feature and annotation are two drastically different functions, but in fact, they are connected. Both are meant to facilitate the writing of weaving messages in a discussion forum. Both features are derived from TextWeaver.
We are in the process of upgrading Marginalia. Some major bugs were fixed. It should be faster. There will be an online help linked right next to the annotation button. With these improvements, we are hoping more people will use the tool and find it useful.
As always, it's wonderful to hear from people giving us feedback on the tool. It is much appreciated.