StickySorter is a prototype application from Microsoft Office Lab. It is a post-it note application with a twist, allowing you "to sift through hundreds of research observations and organize them into groups using a process known as affinity diagramming."
Affinity diagramming may be thought of as the next step to be taken after brainstorming. In it you sort your ideas into groups for further review and analysis. It's also known as the "KJ Method" and is used in project management.
So you can go from this (or something much more chaotic):
All I can say is: it works as promised. I don't know whether I will use it on a continuous basis, but it is a "clean" concept. It's what one used index cards (or sticky notes) for in the "old days." After researching one's topic, noting every fact or idea on a different cards, one sorted the cards into different heaps. The next step was the outline.
Oh ... and it's free!
1. See Kawakita-Jiro-Method, which seems to be a fancy name for what most American children were taught in high school already.