I have 3 mlp OCs now...Amber Dust, Plum Pudding, and Stormjumper. The last two started out as background characters in Amber's life, and as such they aren't as well balanced. I grew to love them, though, and I started drawing them more and more until I had internally developed backstories, personalitites, etc. they started as doodles.
Typically, when I'm making an OC, I try and consider what element of harmony suits them best. That usually helps me develop their character, and it gives me a heads-up to make sure I'm not making a clone of one of the mane 6. 9u9