I prefer my shippings to be as canon as possible, or at least have some decent proof behind them.
Here are my two favorite pairings.
Fluttershy x Discord
Fluttershy is the one who helped reform Discord, and they even go on tea parties! Plus, just watch the Season 4 finale. Discord says "it's mostly for Fluttershy" and makes a squee face, he has a photo of the two of them together, and Fluttershy flies over to him and hugs him when she sees him. Also, Fluttershy cries and Discord later says sorry to her.
Cheerilee x Big Mac
Yes, I know they fell in love because of potion, but the episode was nonetheless adorable and the ending makes me believe that they actually started a relationship together. Furthermore, in Filli Vanilli, Cheerilee swoons when Big Mac is singing and I think that's proof enough she still is in love with him.
I also like Cheese Sandwich x Pinkie Pie, Twilight Sparkle x Flash Sentry, Rainbow Dash x Soarin', and Spike x Rarity OR Sweetie Bell.