(First note -- the problem earlier this week with cards disappearing unexpectedly seems to be fixed with the latest patch. So go download it now!)

I am a graduate student who uses index cards to keep track of research for writing papers. For a couple years, I have been looking for an OS X program to handle this for me, as my handwriting is awful and I have an iBook. I've tried lots of "organizers" such as Circus Ponies Notebook, etc. -- but they never seem to work as I want them to, and I've had to stick with the handwritten notes, or with a Classic program (TakeNote!).

I found SuperNotecard, (then called Miss LonelyNotes) a few months ago, and it soon became apparent that this is the closest program to what I have been looking for. The program's primary focus seems to be fiction, and I have not tried it in fiction mode, but the non-fiction mode is pretty good. Each card has a title and can be linked to multiple References (sources). You can shuffle cards around into different orders to sort your ideas. Cards are stored in decks, but each deck can contain both cards and other decks, so you can have a fairly complicated hierarchical structure if you want.

In this new version, References are more powerful -- you can have the program keep track of things like page numbers, publishers, reference type, etc. (Now if it would just automatically print a bibliography in MLA format...)

You can define Categories for your cards; I haven't used this with much depth yet, though I do have a couple of Categories defined. It seems useful, but I need to figure out how best to use it! :) You can also flag cards, with notations to explain why you flagged them.

This is a good program, with good support (I had a problem earlier this week and they got back to me immediately, and released a patch to fix it just a couple of days later). If you are writing either fiction or non-fiction, it is well-worth checking out.

A couple of comments:

The automatic spell check seems to slow the program down, so I've turned it off. (I can spell check the final paper I write, so I don't worry about the spelling of my notes.)

I wish I could have it print cards in 3x5, 4x6, or 5x7 format, so I could lay all the cards out on the table and shuffle them around the old-fashioned way. :) It would be handy to occasionally have the cards in hard-copy form. Currently you can print the cards on separate pages, or put all the cards on one page, but I would also like to print in the actual card form factor sometimes.

These are quibbles, though. This is good software, and thanks to Mindola for finally filling this need!