The "everything" I use LaTeX. And, in truth, I never regretted this choice. Despite his age (the system was in "early 1980", the first version of the manual comes from 1983) continues to grow and develop your very pleasantly surprised.
But not always need to spend a book or write an article! Most needed are simple notes and enriched only a picture, a screenshot, or - occasionally - the formula.
quite a long time looking for the right tool. I started off came with the system (Ubuntu) Tomboy notepad. Yellow cards are not enchanted me, even though the system somehow "integrate".
For quotations chaotic thoughts FreeMind is useful, which shows the nested list as a beautiful spider (here: Map Mindmap on the program, and here the other maps.
contrast to all other notes, I use Zim . It is This allows a very simple editor (like Wiki) create a tangle of related parties and group them into certain hierarchies. With the right plug-ins may be telling an additional models, combine text with screen shots, include illustrations. Nothing more is needed.
program has its own its own Web server to allow the presentation of information in the form of Web pages. Notes can be exported to HTML and LaTeX. And this latter option is useful to me quite often ...
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