I think Journler is one of the best apps for MacOS X. You can organize everything in there: you can link files on your computer or import them to Journler.
If I am writing about a book that I have classified in my Bookpedia, I simply drag the title from Bookpedia to Journler and it creates a link that open Bookpedia in that book.
If you want to take some audio notes or even record a movie you can do it directly in Journler.
You can make posts on your blog from Journler or send your writings to your iPod.
And, of course, Journler has integration with iPhoto, Mail.app, Adress Book, iTunes, iMovie and so on…
The personal license is donation based and you can check all features here.