I never heard of Notepad Deluxe before. The reason is probably that I did not care much about Mac Software until about three years ago. The software has seen no updates since May 22, 2005. But I recently read Research Journal Tools Reflection: NotePad Deluxe, a post from September 2010 which describes how Michelle A. Hoyle used it for her research. It reminds me very much of Netetab in windows which I still use for an editor.
Much of what she says reverberates—especially her main reason for abandoning Notepad Deluxe: "I also wanted to be able to insert a link to previous work appearing in the notes database. NotePad Deluxe allowed you to insert hyperlinks to websites but there was no mechanism to point to another note from within a note."
This is precisely what lead me to adopt desktop wikis in 2003 and ultimately ConnectedText in 2005.
She promises that the blog post would be followed by others that outline her search for the best research journal too. As far as I can tell, none of these were ever published.