I didn't know WhizFolders. Looks interesting.
Being a note-freak myself, I've tried quite a few options. Evernote is quite good, but it definitely does NOT include the linking to a specific paragraph; in fact, no linking at all (Evernote 2.x did, Evernote 3 doesn't).
Being an old advocate of Linux and open source, and having bashed Microsoft for every poor decision, I must say this: OneNote is my current note-taking solution, and I'm pretty amazed with it.
It lets you link to EVERYTHING, be it a file, a web site (well, that was quite easy), another notebook, another note, or another paragraph, whatever. Even to Outlook tasks and events.
It is not "dual-pane" as WhizFolders, but the paradigm is quite close: on a pane at the left, similar to Outlook's button bar you get your notebooks. Inside each notebook you get sections and even subsections. You can go as deep as subsections in the left pane.
In the main pane you get the sections and subsections on top, and the pages and subpages to the right. And within a page, through indenting, you can get actual outline, collapsible and everything.
It even syncs with Windows Mobile devices. As I said, I am pretty impressed. The official site is http://office.microsoft.com/onenote/
I hope this is useful for you.