We've been thinking about the best way to eventually handle this.. save to a server, local storage or a cookie. Cookies are probably a bad idea though since they can expire and be deleted when the user clears settings.
I'd say local storage, but be able to chose the save path. Then I could back up my save to google drive. Actually if there was a way to save it directly to google drive or dropbox that'd be really cool.
Paul has started a similar project to this with Daedalus. We're bringing it back to PC and adding JavaScipt ans OSX as new platforms. Here's a blog on the JS work: http://n64js.blogspot.com/
At least my google cloud folder has to sync up with the local disk first so it's not really saving directly to it (not sure how dropbox works since I don't have it). I just wasn't sure if you could say log into your cloud storage and allow another website have access to it.