I use DevonThink Pro and Sente. There’s a good trick for using Sente to manage notes on books. Sente will link an indivdual reference to, among other things, RTF files. Keep a “stationery pad” RTF document on your desktop. Each time you want to take notes on a new reference, drop that document onto the reference in Sente.
If you’ve set Sente to manage attachments, it’ll creat a new copy of the RTF file, name it with the book title (or author/date, or whatever you choose) and store it in its attachments folder (~/documents/Sente by default).
Now all you do is ask DevonThink to index that folder. Lo: your notes are accessible in Sente, indexed and searchable in DT, editable in whatever you choose (I use Bean for that sort of stuff) and everything is always in sync. Sweet.
If you’re in this for a longish haul, I’d spring for DT Pro Office and a scanner. That’s what I’m about to do, simply for this good workflow:
(1) Find book in library
(2) Photocopy relevant pages
(3) Scan photocopied pages into DevonThink
You now have text/pdf files you can do what you want with. Very handy.
Good tools now will save you hours and hours later. And advice to avoid: don’t do what I have done and always be on the lookout for a “better” tool. Find a powerful one that works, and stick with it. Nothing does everything and very often the things you think you really want are not things you really need, or things you can do “manually” with a few minutes’ work.
Here’s my ideal academic setup
DevonThink - Omniscient Repository
Skim - marking up/viewing PDFs (better than Preview for extracting snippets by highlighting them.)
Sente - bibliographical management
Tinderbox (For general planning, structuring, working out what you think)
Scrivener (For drafting)
Word 2004 (For final polishing – HORRID app and if it weren’t for the colaborative nature of a lot of what I do, I’d be on Mellel or Nisus like a shot. But alas the rest of the world uses Word.)
A pricey bundle, true, but for an undergraduate/postgraduate trajectory of 6 years it comes to less than the price of a beer a week. Not a lot, in context.