I've been working on integrating Hulu and Boxee into my MythTV setup. I had about everything working, when I needed to correct some remote control settings. As part of that I broke the remote control interaction with Hulu.
After quite a bit of head banging I changed the name of my remote. The original name I had configured was hauppauge_pvr and it was working. Then I found a better config as part of switching to a Harmony remote, but continue to use the Hauppauge remote. The new config used the name Hauppauge_WinTV_Nexus_S, which I found online. That config worked for everything except Hulu. The way I fixed it was to change the name again. I chose "Hauppauge". Sed to rescue on all my configs:
sed': sed -i.bak 's/Hauppauge_WinTV_Nexus_S/Hauppauge/g'
That made hulu work again. My guess is that hulu didn't like the long name .... but that's just a guess.
Once I'm all done I'll put a more comprehensive guide together.