1. Hubbub provides a SAX-style (callback-based) API, while Gumbo gives you a DOM-style (tree-based) struct directly. Hubbub is likely faster in this regard, Gumbo is easier to use out-of-the-box.
2. Gumbo is better tested. It's unclear whether Hubbub's 90% test coverage is "90% of the code is tested" or "90% of the tests pass", but Gumbo has 100% code coverage, 100% of html5lib tests pass (as of 0.95; the html5lib maintainer has pointed out that additional tests were added to trunk recently that don't pass), and it's run without crashing on ~4.5B documents from Google's index.
3. Gumbo has better support for source locations and going between original text and parse tree.
4. Hubbub has character encoding detection, Gumbo doesn't.