For no real reason, here are my favourite ships.
Twilight Sparkle x Trixie
Celestia x Luna
Rainbow Dash x Fluttershy
Littlepip x Homage
Lyra x Bonbon
Rarity x Applejack
Pinkie Pie x Dirpy
Cadence x Shining Armor
Sweetiebelle x Spike
Octavia x DJ PON3 (or RaRa)
Fleur de lis x Sassy Saddles
Sunset Shimmer x Fluttershy (EQG)