I use .txt files; they aren't fancy, but they have many advantages:
- Text files are sufficient for taking notes. If I need a tree structure, I write XML or Markdown.
- There are many free .txt editors to choose from, because it is a non-proprietary file format.
- You'll be able to open them in the next 100 years; they are 100% future proof.
- Most .txt editors have advanced editing features. In more advanced notebook applications, you are constrained to a more rigid structure. For example, splitting up a single chapter into multiple ones will almost always be faster and more convenient in a somewhat advanced text editor.
I'm using jEdit to edit my notes, together with the RecentBufferSwitcher and OpenIt plugins. RecentBufferSwitcher allows you to switch rappidly between the most recently used files (think of Windows' alt-tab functionality). OpenIt allows you to rapidly open a file by name.
I wish I knew a better, more wysiwyg solution but I didn't find any suitable applications. They all had severe drawbacks, such as:
- A proprietary file format, which binds me to a single editor of which I have to hope it will be supported for a long time.
- A rich text editor: I don't want to bother with layout issues when taking quick notes. I only want a conceptual style for titles, subtitles, paragraphs, lists, sublists, emphasized text and links.
Personal Wiki software that uses .txt files for the articles/pages works well with this method. You can either use text editors to edit your .txt notes or the wiki editing features. Some of them are ...
- bLADE Wiki (uses own wiki syntax, for Windows & Windows Mobile)
- Ema Personal Wiki (uses Markdown, for Windows & Android)