The correct answer is Zooey. By far*
*For heterosexual guys. Opinions of hetero women and gay men on the issue of relative hotness of two women shouldn’t count 
It’s like hetero men and lesbians ranking Brad Pitt vs George Clooney in terms of hotness.
Zooey a million times over.
Heh heh… taint.
I have seen exactly one episode of Bones and had to look up the name of the actress because she was in some costume and her magnificent boobies were on display.
So, Emily.
Zooey. They aren’t even close in my opinion.
The same for me, had no idea the girl from bones and th older sister from Almost Famous were sisters. But now that I do, Zooey easily…
Zooey, Zooey, Zooey, Zooey.
I can’t really define it, but there’s something… prickly… about Emily. She grates on me a bit.
Zooey, though, is soft and inviting. She will make me happy. 
I’m a straight married woman, but I totally have a girl crush on Zooey. Mr. Snicks likes her too.
Never watched Bones.
How can anyone hate Zooey?
Now Ben Gibbard - him we can hate.
Zooey. I even liked her as Trillian, which should be telling.
Currently, Zooey, Lilly Allen and Katy Perry are blurring into one (very attractive, slightly quirky) person for me, though.
Zooey, she was so cute in Elf.
Emily does have sharper facial features, and seems to be “harder” than Zooey. Zooey seems softer. But I endorse the Deschanel Sandwich.
I’ll go you one better; I liked her in The Happening, which really took some effort. Zooey all the way.
Zooey. Though my daughter would be totally creeped out by the fact that her father lusts after Lady Larkin.
Superhuman effort. I applaud your fortitude or at least your hormones’ fortitude :p.
Zooey is as cute as a kitten snuggling a golden retriever. But she was as bad as anything in that film. And that movie had acres of badness.
That’s my vote.
That’s how I felt. Finally someone did the “hey you know who her sister is right?” thing to me.
Although…Zooey by a mile.
Zooey.
Emily Deschanel is handicapped by the fact that Temperance Brennan is the most irritating character ever created.
Emily by far. Difference between girl and woman. Zooey is cute, but that’s all she’ll ever be.
I forget that Emily even exists, so Zooey.
Oddly that was her only role that made sense to me. Emotionally unavailable was in the character description and from what I can tell she has all the range of a cardboard box so it just seemed to work. (Sorry Zooey fans)
To be fair, Emily might not have much more range since I don’t know of anything beyond Bones that I’ve seen her in.