Basically, you fire off a message to the server saying that yes JS is enabled. Update the session, and use that from then on in your code.
I am thinking of forking my application in one area where I want to handle things very differently depending on if someone has javascript enabled, and this is the method I think would work best.
The only possible downside would be if someone disables javascript in the middle of their session; however I think the likelihood of that is pretty miniscule. In this unlikely case, you could use a noscript tag to at least notify the user that their Javascript had been unexpectedly disabled, and how to rectify it.
-- Josh