Until now we used zotero. But Zotero has removed the HTML (in version 6). The new editor is really basic (it doesn't even support the font color).
The most famous note taking apps aren't based on HTML but Markdown which is way more limited. (This jsfiddle can give you an idea of the HTML features we need)
- a WYSIWYG HTML editor support
- multi user /multi device editing (=sync)
- hierarchical organisation of notes (and optionally of other entries, like local files(*) )
- html links pointing to others notes from the db.
- the notes should be searchable with keywords and tags
Other features we enjoyed on Zotero:
- (*) entries pointing toward a local file: audio, pdf, video...
- notes could be attached to this entry (eg. a note that summarizes an entry pointing to a pdf)
- support simultaneous editing of notes by different users (like Google Docs)
- html links opening a specific pdf at a specific page (via the zotero://open-pdf protocol)