|Problems? Is your data what you think it is?
I've been using three-ring binders to take work notes for a few years and eventually evolved into keeping a daily work log. Writing paper notes was too slow for me, though, so I started using a text editor and found that was much better.
The only issue was finding things. Searching thousands of lines of notes for a partially common idea or term didn't work as well. That led me to look into using something hierarchical where I can maintain a tree of ideas.
Looking around, I like Treepad Lite (freeware). It's working well for organizing notes, but at the same time it's more work to maintain. I might end up going back to a full log and searching it, or I might end up copying the work log notes into Treepad every week or so to have things organized.