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