I could probably take a guess at 'em.
Twilight: I'm gonna have to say that she would be either Chinese or Finnish. Chinese because of their huge focus on education and excelling grades/performance, and Finland because of their high graduation rate and high quality educational system.
Applejack: You all know what I'm gonna say: most likely American, more specifically Texan, although she could also be Japanese. She fits the whole country girl idea. I mean, she lives on a farm. I'm sure I sound like I'm simply going off of stereotypes, but as a Texan myself, both her lifestyle and personality fit pretty well, although I can assure you her accent is either over-exaggerated or that from another state(perhaps Tennessee, as many of you are suggesting). The reason I also included the possibility of being Japanese is that she has a huge focus on family, one of the more important aspects of life in Japan. They respect their family members, especially those who are older, and they're just flat-out a fairly family-based group of people(not that Texans aren't the same way, which we are to an extent).
Rainbow Dash: I can't really think of something on the spot, but I know a lot of you are suggesting Kenya for their athleticism. Most likely any country with a strong athletic focus and "can-do" attitude.
Fluttershy: I have to say somewhere in Africa, if only for her love for nature and animals. Africa is practically known for its exotic wildlife, with all kinds of animals and plants that Fluttershy would die to meet and see(respectively).
Pinkie Pie: Wow, this one is hard. Maybe Russian, or even Swedish? Someplace known for being outgoing and loud. In fact, she could probably be American, since the U.S. is the "melting pot" after all. Pinkie Pie's crazy nature fits the diversity of the United States' many citizens, so that might work.
Rarity: Definitely some European country, like Italy or something. Europeans are known to be pretty polite and neat for the most part, and some countries are very focused on fashion as well. Almost any European country would work for her.