- Pro - easy to use, chronological view easily available
- Con - math hard to write well, ideas spread over several days hard to view topically.
The other tool I use is a wiki. It's useful to keep data in a structured, hierarchical format that's easy to edit.
- Pro - ideas arranged topically, can do better looking math
- Con - must work topically from the start, no good chronological view (Yes, I know you can view changes in order, but it's not as easy to reconstruct what I was thinking on a particular day.)
I want a single tool that does both of these - that can view the notes both chronologically and by topic.
For work-flow, I want the ability to enter ideas and notes free-form, and perform categorization and annotation at a separate time.
Another additional feature that would be nice is recording other actions on the system (at least by reference).
One example is check-ins to source control.
Another possible example - What if gnuplot were to record all the commands issued (and kept a copy of all the files used?) Graphs could be re-created and played back at a later date easily.
I looked around a little bit to see if there are other applications that might meet some of these requirements (or at least be an improvement over text files and a wiki). One class of app is a note taking application. I looked at Tomboy. It does have a Latex plugin (though I could not get it to work). Latex side-rant: It's great for making nice looking mathematics, but you wind up with "equations under glass". It's pretty to look at, but you can't manipulate it further. For mathematical content, I want something with more precise semantics (Content MathML, for example)
Another class of tool is mind mapping software. I looked at Vym (View your mind) briefly, but I don't think I will like this type of software. Viewing a graph of links is nice, but not as the main working view - I prefer a wiki view (pages with links)