Sciplore has produced an interesting hybrid between a mind mapping and reference management tool. Freemind Scholar adds two basic features over the excellent Freemind: you can have references (at this time, only bibTeX) inserted, and you can drag and drop hig hlights on pdfs (the pdf is linked).
This looks like the perfect IDE for sketching notes while reading papers. I use oneNote for this, but I’ve tried mind maps before and could easily revert to it.
As soon as they implement zotero/endnote references, I can imagine many people finding this tool very useful.
Freemind Scholar is in alpha right now. Feel free to try it out and send them your comments, chances are they will implement your feature requests since they are just starting.