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TreeSheets (Cross-Platform Data Organizer) Now Open Source
Aardappel writes "TreeSheets has been available as freeware for Windows / Linux / OS X since 2008, but is now also Open Source (ZLIB license). TreeSheets is a cross between a spreadsheet (you can create grids) and an outliner (you can create grids inside grids) allowing you to create almost any structure to organize your data in."
As much as I hate to say it, Microsoft One Note is probably the best there is.
I ended up mainly using it as a tabbed graphics program. Since it remembers individual pen strokes, it's possible to copy a circuit diagram, remove the part the professor changed, and then draw the new changes.* Combine that with engineering paper grids, handwriting conversion, drag and drop picture embedding for annotations, and an intuitive navigation system for changing between courses and it's a necessity.
If you're talking Linux, then you're, sadly, out of luck. I haven't found anything that even comes close. One Note doesn't run in wine, and the license file is a pita to fix if something goes wrong in Windows. For all those faults, it's an amazing piece of software, and I can't find anything better. I'm currently trying to get it to work in an XP VM on Kubuntu.
*Note to professors: When you modify a circuit, give your students time to copy it from scratch, instead of immediately going on. I bought a tablet PC just for this reason.
PS: Ehh, who needs mod points.
So lets pretend that we've just completed writing this code, as opposed to having just completed sabotaging it -Altera