As I noted recently in the discussion on plain text vs. notes/writing apps, I settled on HTML in TextEdit as my preferred note format for my journal and personal hypertext system (which I also browse in DEVONthink), instead of RTF. It is functionally identically to RTF, providing rich-text features like multiple highlight colors and text colors etc. (but no inline images in TextEdit—I just link to images as sidecar files).
I consider HTML to be far superior to RTF when I want do batch search-and-replace across multiple files using regular expressions (which I typically do with BBEdit’s multi-file search, when necessary). Parsing HTML is super-easy (especially if you’ve been working with HTML most of your life, as I have) but parsing RTF is a horrific nightmare (in my opinion).
I wrote an AppleScript service that I invoke with a keyboard shortcut that creates a new HTML note and opens it for editing in TextEdit. I wrote an AppleScript droplet that I drop files onto when I want to create hyperlinks in my notes.
I’ve been happily working this way for about five years and I don’t anticipate changing. I use plain text for some purposes, but usually I want all the features that rich text provides (but with the underlying clarity of HTML, not the forbidding mess of RTF—just my opinion of course).