I never liked the idea of HttpOnly for cookies as it prevents my favorite way of stopping another increasingly common class of attacks known as XSRF.
When HttpOnly is NOT enabled, a developer like myself can post the cookie as POST data in an AJAX request or whatever in order to show the server that the request came from the appropriate domain. It’s usually called a double submitted cookie, and it’s what allows applications like Gmail to ensure that the visitor who is making the request really is trying to make the request (as opposed to some evil site who is trying to grab a user’s address book by including a script tag on the page that references the script dynamically generated on Google’s server for that user). Another example of an actual XSRF that could have been prevented by using doubly-submitted cookies without HttpOnly can be found here: http://www.gnucitizen.org/blog/google-gmail-e-mail-hijack-technique/.
Anyway, like Chris Dary said above, This trick, while definitely useful, is treating the symptom and not the disease.