According to the source:

Here’s the data anyways for the 20 most popular “Shipping + Character X + Character Y”.

PinkieDash – 124

TwiDash – 124

AppleDash – 123

FlutterDash – 114

RaritySparkle – 111

RariJack – 109

TwiJack- 108

FlutterSparkle – 108

PinkieSparkle- 107

RariDash – 106

FlutterJack – 103

RariShy – 102

ApplePie – 100

FlutterPie- 100

Rarity/Pinkie- 97

Twilestia – 36

TwLuna – 36

CelxLun – 30

TwilightxOC – 28

AJxOC – 27

Percentage of X Character stories are also tagged with Shipping (25 stories of Character or more)

55% Big Macintosh

28% Rainbow Dash

26% TG&P Trixie

25.5% Applejack

24% Spike

24% Fluttershy

24% Rarity

23% Twilight Sparkle

22% Pinkie Pie

21% “Other“

20% Princess Luna

17% Applebloom

17% Princess Celestia