I just switched back from NotationalVelocity to DevonThink Personal Edition - the big reason? DTPE now has automatic (as well as explicit) linking between entries, in wiki style. And a whole bunch of new features, too. Sweet.
Now, if only it would get the auto-find-on-keystroke interface (like Launchbar or Quicksilver, but just for the content in the app) done like NotationalVelocity has... That would be the perfect personal content management system...