Hi Darren,
Thanks for your comments. Bookends UI has evolved a lot in the last few years, and it will continue to do so.
I'm not familiar with IdeaMason (although I peeked at their web site), but writing/organization tools on the Mac that I know are popular with Bookends users include Scrivener and DevonThink Pro. One (or both) might be useful to you, too. Why not create a new forum topic asking other users what they recommend (I'm afraid many won't see this since it's buried in a thread on the new web site).
Jon
Sonny Software