I'm minutes away from giving up on IdeaMason. As noted by others in this thread, it's quite inflexible and, as far as formatting features go, it's very limited. I am going back to my roots - Word and Endnote and done with it! This obsession with software driven "solutions" to everything is costing me my PhD! Time to rein the obsession in and re-focus my energies. If I am doing things "right" my participation here will be curtailed as well...
That's what I ended up doing in June 2007 : MS word (can't go wrong with it -- but if that's not good enough, there's oo.org and textmaker ), endnote, X1+Archivarius+farr, EverNote** for quick ideas or clips, AND a good naming scheme
(all important metadata in the filename, no more complex directory structures, no more tagging software).
** I don't use EverNote anymore, I've switched to SQL-Notes. Still in beta, but with more possibilities and with a developer that's willing to make it HAPPEN... The imminent MS word integration (which will replace the actual HTML pane - around March 15) will probably allow one to do almost everything IdeaMason can't, and more, MUCH more (it'll take a bit of configuration work of course; but once that will be done...). Hypothesis : combining MS Word and
probably means that Endnote's MS Word plug in will work within SQL-Notes "MS Word Pane". Maybe.
PS : Darwin : my guess is that for all your scientific research and data, SQL-Notes database and infinite fields creation capability + formulas and scripting, would be much more efficient than ideamason or even OneNote and it's "obscure" file format. SQL-Notes will be able to work with different database backend.