>Cultural
Rainbow, Twilight and Pinkie. The ones I see people always recognise. Amongst online types, they tend to know Twilight but more because of her being the face of like 15ai and stuff? Wonder if Southerners are more likely to know Applejack or something. Amongst regulars, Rainbow/Pinkie. Celestia deserves a mention too just because of the FiO fags and their small wedge in those sorts of communities.
>Characterisation
Probably Rarity doing the best. I'd say Twilight fared the worst in that regard though, completely atomised and she's practically 2 different characters (and if you're into the Unicorn side she's about as popular as Applejack at this point.) and a lot of people treat here more as an easy plot-mover-forward figure as opposed to really touching on her character. Sad!
Fluttershy, too. Especially since IIRC she used to be the most popular.