Is there a good freeware / open-source tool to manage user stories in terms of capturing and tracking stories that are currently being developed?
Nearly all of the free project tools for "agile" methodologies out there do model user stories. Such as Agilo for Scrum, XPlanner, and so on... And perhaps Mingle, but that is not free.
(-or does "capturing stories" mean something else in your context, other than short pieces of prose?)
Scrumy has a free version that gives you user stories, todos and a virtual taskboard.
With the free version, you do not get a backlog or protected access, but the paid version is about $7 a month. I have been using it for a couple of months and find it to be well worth the money.
Mingle is free for open source projects. There is also Pivotal Tracker.
More and more issue tracking software supports Wiki markup languages, so that is really excellent for authoring user stories. This is what I use. I record user stories and such as 'trackers' and I use the description field that support textile for the user story.