Ah thanks for the tips. Zim looks really nice in that it has a calendar and that you can change the name of the links, something that used to bug me. If only I had had the time to code in a plugin to put the notes onto a scrum board it'd be so good.
I get the feeling that microsoft's one note is somewhat inspired by Tomboy, it's not that bad actually. Even though it doesn't do links in that sense I feel it's the closest any other project have come. Apart from the open source solutions of course.