Favorites lists seem to be the trendy thing to do, so I will start off with the basics. These are my favorites of the Mane 6 in order of preference, 6 being least and 1 being my most favorite.
1.) Pinkie Pie: Pinkie is the class clown and can perform both physical and visual humor as well as one-liners with ease. She's not just comedy relief... most of the time she is the comedy. She is always eager to make her friends laugh and goes to great lengths to make new friends and, as we all know, friendship is magic. Whenever her mane loses its bounce it hits me right in the heart.
2.) Rarity: Rarity has grown immensely as a character since her first appearance. Initially she seemed to be just a shallow egotist, but her generosity always wins out over her personal interests. Though she does not have as many family members appearing in episodes as the other characters, she has displayed a strong sense of family values when interacting with her sister. She is strongly loyal to her friends as well, perhaps just as much so as Rainbow Dash.
3.) Applejack: A hard worker who is faithful to her family, Applejack is a good role model in this group. However, sometimes her pride is as much a flaw as it is a strength. And though it doesn't happen often, I sometimes sense that the writers want us to think she is less intelligent than the rest of the group. I won't clutter the page with specific references, but it's just an overall feeling I get when perhaps they are just trying to emphasize her down-to-earth nature.
4.) Fluttershy: One can't help but adore the mild-mannered and soft-spoken lover of nature and animals. But for the most part the writers have over-exaggerated her timidity in my opinion, often to the point that it is crippling to her, and this keeps Fluttershy from being higher on my list of favorites.
5.) Rainbow Dash: Put simply, Rainbow is competitive and arrogant to a fault and I find her over-inflated ego annoying, just as I dislike this quality in people. Her loyalty to her friends is admirable and certainly a redeeming quality, but that alone isn't enough to earn her a higher ranking on my list.
6.) Twilight Sparkle: This Alicorn Princess ranks at the bottom of my list because, despite her obvious humility where such things as her title and abilities are concerned, I have had a feeling throughout the series that things have just luckily gone always in her favor and that she has been awarded the things she has as much through the efforts of her friends as by her own virtues. This isn't her fault, and I dare say it's mostly due to the bidding of Princess Celestia as she maneuvers Twilight and her friends a bit like pawns. But in the end, it will take more than humility to get Twilight off the bottom of my favorites list.
So there you have it. Please feel free to comment with your own opinions, whether in agreement or disagreement... I'm sure there will be plenty of both.