Well this one is tough, but I'm going to go in order from first to go to last:
1. Rarity
2. Applejack
3. Fluttershy
4. Rainbow Dash
5. Pinkie Pie
6. Twilight Sparkle
Rarity dies first because she may have some magic but she doesn't know many spells, and doesn't know any other form of combat.
Applejack may be in great physical condition, but she cannot fly or use magic. At least she knows some combat.
Fluttershy is capable of flight and has control of the woodland creatures in Ponyville, her personality is the limit to her power though, still even with a more bold personality she wouldn't be ranked any higher on the list.
Pinkie Pie could easily defeat everybody in mane six, but due to her slapstick personality and habit to be easily distracted, she could only go so far.
Twilight Sparkle wins this battle because like Pinkie Pie her power has no upper limit, but she uses magic rather than randomness to perform incredible feats, she could make herself lose control by the time the first 4 are dead and have nothing holding her back from destroying everything.
There you have it, my opinion on who would win in a battle between mane six.