Allow to attach (several) tags (key words / categories) to a note and to search / classify notes by them.
organizing ideas in tree-form offers great level of freedom, but . . .
How about adding a possibility to attach tags (keywords) to a note?
By organizing notes in tree form a note can belong only to one category, defined by a corresponding tree node,
by attaching several different tags it becomes a member of several different categories.
Example: a note about a software product can be tagged e. g. :
Microsoft, software, graphics, multimedia, bitmap, freeware
and found by any of this tags (categories).
What is more important,
all other related notes (members of a category) are immediately found and displayed too.
See:
Mozilla Firefox - bookmarks tagging
and/or
CintaNotes - a PIM based on tags only (no tree at all, but much more flexible, IMHO)