I use TodoList for tracking during design and actual development. It is a simple hierarchical to-do list, but also offers basic project management features (i.e. setting deadlines, priorities, and categories and tracking progress for tasks). Files are XML and can be easily processed and versioned, and it includes some basic collaboration features (although I haven't used this yet).
When collecting a large amount of information, especially if it is primarily text, tables or images, before actual development or brainstorming or just recording thoughts, I actually use Microsoft OneNote, although I would not install it just for that. But since it is included in Office, which is installed on all computers in my company, I use it because I am quite comfortable with it. I use OneNote only for myself, although, like, well, a notebook.
Oh, and then, for information that is actually not for one project, but rather for reuse, we certainly have a Wiki, although it’s sometimes difficult to convince people that they really use it (“what, wiki? I just call you when I need this information! "). Sigh.
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