This year I'm a supporting member of WorldCon for the first time, and I noticed that the Hugo's have a category for Best Fan Writer ("Any person whose writing has appeared in semiprozines or fanzines or in generally available electronic media during 2010."). I do believe Harry Potter and the Methods of Rationality counts, and I plan on nominating it. Even making it onto the ballot will probably expose it to a wider audience. Is anyone else here a WorldCon member and thinking of nominating MoR?
I'd planned to try and get HPMOR nominated for Best Novel in the 2011 awards (which will be awarded in 2012). I'm not sure if my personally being nominated for Best Fan Writer makes the work ineligible, or if it would be considered bad sport to try twice.
You could still put "Hugo-winning author" on future books whether you got Best Fan Writer or Best Novel - and you have a higher probability of getting Best Fan Writer. Remember the Hugos are a popularity contest.
I think I've seen the same work nominated in separate categories in past years. Not sure. Ask Keith Lynch.