This is a small area, but it deserves some attention because of a few outstanding programs I must gush over:
Simple mind mapping utility. Pretty useful for minimal mapping, KDE standard.
As the name implies, VYM is a similar mind mapping utility. It lets you customize the shape and function of your thought bubbles, use multiple pages of diagramming, and is a fun distracting way to prepare for a project or paper.
I adore mnemosyne. The utility of this program is apparent for classics and mythology fans as it references the Greek goddess of memory. With this program you can enter flashcard information for any subject (foreign language learners are the key audience.) The program will give you flashcards and an accompanying rating system which allows you to rank your knowledge of the featured card. This will be documented and using that ranking, you will see the card more or less frequently. Additionally, it keeps statistics for your performance and can tell you according to category (in my case: Latin Grammar, Latin ch. 23, Latin ch. 24, etc.) with what subject you’re struggling the most.
A beautiful idea with an equally beautiful execution. Databases for languages more commonly acquired than Latin are available on their website.