Today I found a notepad type app for OS X that is the closest to what I've been looking for in a generic note-taking app. It's called VoodooPad. Here's a bit of the description from the product page:

VoodooPad is a new kind of notepad. It's like having your own personal hypertext library, where you can jot down notes, web addresses, to-do lists... Anything on your mind. VoodooPad automatically links each page together, to form a miniature world wide web, on your desktop! Anybody familiar with the WikiWikiWeb will feel right at home with VoodooPad.

I love the whole Wiki aspect of it. It's kind of like having a personal single user Wiki for taking notes.