Lauren Faust and Cindy Morrow dropped a bunch of MLP behind the scenes stuff over on their Twitter pages, primarily dealing with original ideas and the first two seasons.

*Applejack's Dog Winonna was originally named Brandy, then Buckaroo
*Gilda was originally named Grizelda
*Suited for Success was originally called Dress for Failure
*Applebloom was originally named Appleseed
*Big Macintosh was originally Big Apple
*Sweet mela, apple Acres was originally Big mela, apple Orchard
*One Bad mela, apple was originally Bully For You
*Carousel Boutique was originally Carousel Couture, and was an actual carousel with moving mannequins for Rarity's designs. Unfortunately the idea was rejected.
*Ponyville was originally Fillydelphia
*Celestia was originally Queen Celestia, and *Nightmare Moon was Discord
*Opal Essence was originally Ruby, but many gem stones are already trademarked for toys
*Twilight Sparkle was originally Twilight Twinkle. Lauren actually wanted to name her just "Twilight", but there were legal issues there. Twilight Twinkle was also lacked due to the same legal stuff. No subtle jab at the Twilight Saga was used in the making of her final name.
*Rarity's Element of Harmony was originally inspiration
*Twilight Sparkle originally had dark blue hair with a light blue stripe
*Diamond Cani names are Fido, Rover and Spot (which has been revealed already)
*Pinkie's Sisters weren't named, but ideas of Mince Meat Pie and Chicken Pot Pie were floating around.
*Zecora was originally named "Shaman"
Bird in the Hoof was originally concieved as a tug-at-your-heartstrings style episode about losing a pet
*Golden Oak biblioteca was originally The albero of Knowing
*Pinkie Pie used to have a "Sugard Rush" power when she ate too much candy. She would plow through doors, and the Cakes had to replace theirs on a weekly basis
*Rainbow Dash was originally a serial prankster, and Rob would mistakenly call her a "he" in meetings
*Luna's original name was Selena
*Scootaloo was originally supposed to get in a lot of schoolyard fights over not being able to fly
*Luna Eclipsed had a scene with Rarity making a rosa princess costume for Luna
*In Return of Harmony applejack was scripted to climb to the superiore, in alto of the balloon to get to the basket to rope RD.