I found Temple of Doom more enjoyable than the third, and Fate of Atlantis is one of the best LucasArts adventure games.
I have some regerts with my list too. Nice to see Doom II at the midway point on an RPG forum though. Can't wait to see how Alpha Protocol does.
I did play some of Hyper Light Drifter, but I wouldn't recommend it to someone who wants more Hyrule Fantasy, that's what Zelda Classic is for.
I need to get back to Shadowrun Returns as well, got to the matrix. I'm having a hard time finishing NWN2 right now though; too busy playing my Doom II backlog.