Okay, I'm sick enough to give some actual thought to this
Twilight would die first.
Cause of Death: "1000 Things to do Before You Die," is the name of the book she read before she went skydiving, which was number 421, I believe. Her parachute was not properly packed, did not open, and she fell to her death.
Then, Pinkie Pie
Cause of Death: Diabetic Shock. All the years of sweets consumption will finally catch up to her and her pancreas will give out, sending her in diabetic shock, inducing a coma she won't be able to come out of.
Next, Rarity.
Cause of Death: Sewing Machine Malfunction. Her sewing machine ends up sewing her to her newest creation, the needle stabbing her through the eye or right through the head, instantly killing her.
This saddens me... Applejack.
Cause of Death: Crushed to Death. By a tree. Come on, after being bucked so many times, one of those trees is sure to give out after one kick too many. Big Mac, he might have been okay, but Applejack's whole body would be crushed. Spine severed and all vitals turned to mush.
Rainbow Dash is next to last.
Cause of Death: Impacted Skull. That's right. She flew fast, but didn't look where she was going, and her busted her skull wide open ramming herself into a building.
And last... Oh god ... Fluttershy.
Cause of Death: Heart Attack. Come on, she's such a scaredy cat sometimes, you all agree even if we love da Shy. Her heart's had one scare too many, and fails after stepping hoof outside for the first time since the death of her friends. What scared her? Well... Let's just say the leaf that blew in front of her is being prosecuted for ponyslaughter.