DISCLAIMER: These ships are mine. I am not enforcing them on anyone else. I like these characters together and see many possibilities with them having a romantic relationship. If you do not like these characters together, that's alright. You can have an opinion as I have my own.
Let me say it again: these are MY ships.
But I'm still gonna get lots of angry people on this one, aren't I? Oh, well. Relationships are actually a fun thing to have entertaining arguments over.
Anywho, here are my personal ships for MLP:
1. Twilight Sparkle x Star Tracker
* I'm personally not a fan of Flash Sentry and love the relationship that Twilight and Star Tracker gained in "Once Upon a Zeppelin" instead
2. Starlight Glimmer x Sunburst
3. Rainbow Dash x Quibble Pants
4. Rarity x Bellhop (the pony from "Rarity Takes Manehattan")
* This one will probably be the most confusing since Bellhop is not really even a secondary character, but I think Rarity falling in love and marrying a manual laborer would be interesting.
5. Cheese Sandwich x Pinkie Pie
6. Applejack x Spike
7. Discord x Fluttershy
Again, you can disagree with my choices, but these are my personal favorite "ships".