Ooooh yes....this thread. >:3
Twiluna-
I think after Twilight saved Luna from herself, Luna began to develop feelings for her savior despite a little initial jealousy that she and Celestia were so close. The initial courting would be so funny, with Luna basically asking for Twilight to be her suitor in front of her friends in a grand fashion and wondering why it was so weird to make a big deal of it, not realizing dating was so lax now. Twilight says yes, of course. Que lots of stargazing and cuddling and eeee.
Rariflutterpie-
Ah, yes, my ot3. I just think the three of them work so well together. Fluttershy is the middle of the pony sammich, so to speak. Fluttershy needs Pinkie to learn how to be more outgoing and to have fun, and she needs Rarity for the more relaxed moments (she really enjoys their spa visits!). Pinkie brings chaos to the house, but Rarity secretly enjoys it and draws a lot of inspiration from the party pony.
Appleseed-
Yes, I know that they're cousins...which might be odd if they grew up together, but they didn't. Being almost complete strangers, Babs develops a crush on Apple Bloom, admiring her perseverance and ingenuity. Likewise, Apple Bloom admires Bab's softer side. After Bab's leaves Ponyville, she begins to stand up against bullies back in Manehatten, defending the weaker of her classmates.
There's tons more but...I'm lazy. Dx so have my top 3 ships.