I am using Zim desktop wiki extensively as my note taking tool. To quote their website, “Zim is a graphical text editor used to maintain a collection of wiki pages. Each page can contain links to other pages, simple formatting and images. Pages are stored in a folder structure, like in an outliner, and can have attachments. Creating a new page is as easy as linking to a nonexistent page. All data is stored in plain text files with wiki formatting.” Attached files are kept in sub-folders. This means you have access to all your text and files, with or without Zim.
There are various plugins that provide additional functionality, including a task list manager, an equation editor, and support for version control. One very interesting plugin is the GNU R plot plugin. It offers a simple dialog that allows you to insert plotting scripts in GNU R’s language.
For example, typing the following code in the plugin dialog:
x = seq(-4,4,by=0.01)
y = sin(x) + 1
Will give you this plot in your text:
Check out the plugin’s help page for more details