Denham provides a nice little list of tools that people can use in response to a question on Brint: Tools for annotation.
These include wiki, AskSam, blogs, personal databases, Biblioscape, QuickTopic. He also adds some items to consider around where the notes will be kept and who needs access to them.
I would add some other tools:
- MS Outlook's fine Journal facility. I use this for nearly all my notes with phone calls and meetings. Not quite web annotation, but very handy, nonetheless.
- PersonalBrain (click on Personal Solutions) is another great tool, if you can get used to the navigation. I drop nearly all my research notes, whether web-based or paper. Search capability is fair.