I'd suggest jingo thanks to its nice design (with very sane typography), use of git as backing datastore, format compatibility with the markdown format used by github (gollum), and the fact that it's somewhat actively developed.
As of Jan 2017, Matterwiki is also actively developed.
Wiki.js is also being actively developed. It's using a git datastore, has a markdown editor, search engine and assets management.
Tiddlywiki can generate static HTML.
Npmjs and GitHub reveal only two other relatively popular and somewhat active projects: openKB and Hazel.
Wikipedia shows mostly the same JS wiki engines, plus Grokla, which is closed source.
Wikimatrix lists 7 wiki engines powered by JavaScript.
Old answer: https://github.com/gjritter/nodewiki (no updates since 2010).