I am big fan of Linux/Ubuntu so using open-source Zim editor for diary keeping or recording notes for anything new things i learn day to day. Although files are in txt format and contents can be seen in normal text editor, but zim inserts its own markups for better formatting. If you want to view files in better way, Zim can be installed and these files can be opened. Please be aware, these notes are for my personal references and can contain few typos and incorrect english.
For each topic, I tend to read from various sources and record my findings/understanding with links to resouce in the topic file. At the bottom end of topic file, I have todos and questions section