(I am a bit baffled that Midnight, which I thought was the best episode on first watching, didn't make the cut for the Hugos. On the other hand I have now acquired the other three non-Who nominees and intend to watch them in due course, which will be interesting as I have literally never seen any Lost or BSG).
(Also just to note that I enjoyed The Unicorn and the Wasp even more the second time round, and that they were entirely right to drop the framing device of Old Agatha reminiscing. I'm glad I've seen it from the DVD extras but even gladder that it wasn't there to clutter up the broadcast version.)
Unlike a lot of people I wasn't overwhelmed by Silence in the Library / Forest of the Dead. On re-watching, I enjoyed it more, but still feel it is weaker than Moffat's previous New Who stories. Perhaps I am being unfair, and I guess that expecting another Blink is not reasonable. I must admit that as sf, its concept works very well - the intersecting levels of reality, the time-traveller who meets a lover from his own future; and as drama it is pretty effective, with Alex Kingston and Catherine Tate particularly strong, and the utterly horrible creepiness of the ghosting data chips ("Who turned out the lights?", etc).
My two problems with it are both to do with River Song's story. To get the easier one out of the way, her ending is not a particularly happy one; she is still dead, and gets to spend an ersatz afterlife in the computer's memory with her crew rather than with the man she loves. (If you work or have ever worked in a team with other people, just consider for a moment whether you would prefer to spend eternity with them or with your lover.) The script didn't quite do justice to the tragedy of River's story for me.
My other problem is that while the story works as sf and (apart from the above niggle) as drama I'm not so sure it works as Doctor Who. Back in 2006 I enjoyed The Girl in the Fireplace, but rated it below School Reunion, because one of my sources of enjoyment in Who is its dealing with its own mythology, and another is the relationship that we as viewers build up with the regular characters, and TGitF did not deliver much on the second and nothing on the first of these. Now, where at least TGitF had a decent start and closure to the Doctor's love story, with Renette's death ending their relationship, SitL/FotD cheats us because we are asked to care very deeply about the Doctor/River dynamic, without getting the payoff of it becoming a regular plot theme. (No televised return to explore River's past relationship with the Doctor seems likely now, and anyway it would hardly get satisfactory treatment in the time we have left.) So while this episode may well get strong support from Hugo voters who are not regular Who watchers, I was and am surprised by the favour it has found among fans.
So I am really rather agnostic at present as to how I will cast my own Hugo vote in this category. I still have some time to decide, of course.