A large number of applications, some of them extremely complex, could be summarised as "entering text". It's generally more important what happens to the text after it has been entered. In this case:
- Hyperlinking between documents and sections of documents(without needing to use a full relative/absolute path)
- Visualisation of the relationships between documens
- A metadata schema for documents(title, summary, tags, etc.)
- A search engine which indexes the content and metadata
- Embedding of various content types(other notes, diagrams, images)