My vision for notes would be similar to the way Microsoft Word handles change tracking. Bubbles in the right margin that are "attached" to verses or words within verses, that expand and contract dynamically to best use the space. They would also have formatting tools (like highlight, underline, etc), would allow hyperlinks to verses or to external sources, and would allow icons to indicate the type of note it is (like cross-reference, definition, person, place, quotation, question, etc.).
Oh wait, I'm describing new editing functionality... for the print part, just putting the notes in the margin and visually connecting them to the verse or words they relate to. I agree with Eric that I do not want my notes to interrupt the text.
Thanks for listening!