I love Coraline but in my opinion it's too tied to the book/movie (so I guess that being a good or bad thing depends on your opinion of the book/movie). I think it definitely would get misread as Caroline a lot, that happened to the character in the book. It's a guilty pleasure for me because it would get misread so much and I don't like the fact that the author just made it up. I love Cora and a bunch of other full names for Cora, though - Coralie, Cordelia, Corinne, Corabelle, etc.
Coraline may have the same pronunciation problems as Emmeline. It will probably be pronounced as "line", "leen" or "lyn". In spite of this issue, I think Coraline is the more versatile name as it would give you the option of using all three choices (Cora and Coral as nicknames and Coraline on the birth certificate). Do make sure you don't like any other girls names ending in "line" before you make your final choice. :)
Neil Gaiman thought he made the name up but then discovered that it was in fact a legit name with a history (he mentioned this in some interview awhile back). So while the book and movie definitely made the name more mainstream, the name didn't originate from them.
Anyway, I would go with Coraline since you can use both Cora and Coral as nicknames. Unless you want to use a super long middle name, in which case I'd go for one of the two shorter names.
Cora, I like the simplicity of it.
My vote goes to Coral. It's most beautiful to me cause it feels naturey and vibrantly colorful. I never saw the movie Coraline, but somehow associate it as being gothy...I could be wrong, but that's my memory of it. Tim Burton or something? A cartoon, no? I would rather a name evocative of sunny brightness & the ocean, but that's just me. Cora is very sweet, but prim. I picture a Colonial girl & I think of the name Laura which I associate as shy & sweet.