Jon,
I think a lot of what you've said sounds great. Here's some of my thoughts:
I think there may be something here (but I'm not exactly sure what). The notion of allowing users to create (and edit) text notes might be useful.
I think one of the biggest benefits is that something like this would allow Bookends to become a little more functional as a stand alone bibliographic & note-taking app., and that might just fit the real needs of some, if not many, users. Sure, a lot of Bookends users use BE with DevonThink (or similar apps). However, some of us do not, and don't really want to add another app to our workflow--at least at this time. In any case, for those who don't need all the functionality of a DT-type app, Bookends would be the only reference/note-taking app they would need. Yet, for those users who do need a DT (or for those who eventually do, but don't just yet), what you've mentioned would still allow for the notes taken in BE to be indexed or copied to DT. In short, individuals like homeschoolers, undergrad students, or users with more modest needs could start collecting and taking notes on references in Bookends, and might never need anything else. Yet, if they eventually did, then they could "upgrade" or "graduate" to include something like DevonThink into their research workflow.
I'm not sure if the attachment inspector is the best place (although it makes sense). Why not in the List View lower pane (where attachments are used)?
Sounds great to me. I was just playing around with the inspector earlier today and noticed that attachments show up in a hierarchy, and then thought to myself, "hmmm . . . what if . . ."

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The new text note would simply be a text file (it might automatically receive the name Bookends would ordinarily assign an attachment plus the word " note"
Something like that sounds good, too. I would say, it would be good to be able to modify that identifier (ie. be able to manually change it to end with "quote" "Key Point" or whatever).
Or, even better, if you're thinking about adding some kind of pop-up menu item, down where those other menu items are, at the bottom of the list view, you might just as well be able to add some kind of user-identifiable choices. Kind of like how a user can add a new source name in the Preferences, but here a user could add a new kind of "card" or "note card" name.
Additionally, maybe when a new type of card is created, a default folder for that type of card is created as a sub-folder for that reference (kind of an expansion on what you mention below). Thus, just as in the Preferences there are several pre-named reference types, and some user-namable reference types, there might, too, under the Preferences be a tab for "note cards" with one pre-named "notes," and a few more options that could be named whatever the user desires. Then, if/when the user actually creates one of the various types of "note cards" Bookends would pick up the name of that type of note card and create a sub-folder for that reference with that name (ie. "Adams & Smith 2004 notes" or "Adams & Smith 2004 quotes" or whatever). Finally, whenever the user created an additional "note" or "quote" or whatever for which that type of note card has already been created, the additional "note" or "quote" or whatever would be automatically filed in the correct corresponding sub-folder.
Regarding the note cards being automatically appended like you mentioned (ie Adams & Smith 2004 note), would it be possible to make successive text notes to be additionally appended with a number and ordered as such (ie Adams & Smith 2004 note1; Adams & Smith 2004 note2; ect)?
This would automatically be placed in the default attachments folder. Perhaps is a dedicated subfolder called "Bookends Notes"? You can already use Spotlight in Bookends to search for references with attachments that match in the default subfolder.
This would mean that all notes would be in the same default folder subfolder. Alternatively, Bookends could display the usual attachment dialog and let you put it anywhere.
All that sounds Great!
The comment about adding a link from the "card" to the original reference makes no sense in this scenario, because it's not a "card", just a text file that can be opened in any text editing app.
I think the files being just text files works great. Again, if someone really needs the power of a DevonThink (now, or in the future) they can upgrade to DT, either index or copy the sub-folders and text files created in Bookends to DT, and use the existing functionality within BE to link to DT. Also, as MetaData becomes more refined, something might be able to be added then, but for now, for simple--but effective and usable--reference management and reference note-taking, I think simple text files and simple folder hierarchies would be great!
What are your thoughts?
Well, that's my 2 cents worth. Again, I don't know if any or all of this is feasible. But, it sounds like the functionality is nearly there, and if so, then BE could become a simple, one-stop reference management and note-taking app!
Thanks for listening, and for seriously being open to dialogue with your users. I don't know what your personal story and background is, and I don't have a lot of dealings with software folks, but I'm being honest when I say you're just about the best software tech/developer I've run across. Your attitude toward, and responsiveness to, your users is very impressive! And I'm sure I'm not the only one who believes that.
Blessings,
Tony