These are my opinions and my list. It may/may not match yours. I respect your opinions, so please do the same with mine!
1. Rainbow Dash - I like how feisty she is and the way her character was designed as well as colored. She's not perfect by any means, but no one is perfect!
2. Fluttershy - She's cute. I want to just hug her into oblivion. I love how demure she is portrayed and I like her as much as Rainbow Dash (maybe an attempt to balance them out in my subconscious as they are the opposite of each other.)
3. Twilight Sparkle - I like her because I like magic and I also like how intelligent and dedicated she is. Purple is also my favorite color, so that always helps.
4. Pinkie Pie - I love how off the wall she can be. Sometimes I get like that too. She used to be my least favorite pony, but started to grow on me as time went on.
5. Rarity - Well she's pretty! I can't really find a way to relate to Rarity sadly, and that is why she is low on my list. She is a little too spoiled for me, but don't get me wrong. I still think she is OK.
6. Applejack - I also can't relate to Applejack at all and that is why she made the bottom of my list. She has great redeeming qualities, but personally her character as a whole doesn't appeal to me for some reason.