Book on a Stick is a modified version of Wiki on a Stick, that is, a wiki that "lives in one self-modifying XHTML file." It is clearly inspired by TiddlyWiki. In fact, Book on a Stick even uses the TiddlySaver.jar.
It uses WikiCreole as its markup language. But it also can do footnotes—sort of.
I dislike the editor because it is looks very busy:
An interesting application. It won't me make switch, however.
1. See also WikiCreole on Taking Note.
2. It does not help that the footnotes appeared on the top of the page when I tried it out. But I was able to change the CSS entry for the footnotes from "margin-top:-3em;" to "margin-bottom:-1em;" This makes the footnotes appear correctly.
3. Also, it seems that you cannot save entries in Chrome.