Wolf O'Donnell from Star Fox tf'd into Isabelle from Animal Crossing is an idea i've had in the back of my head for a very long time.

Gilda from mlp becoming a nerdy and or dweeby unicorn pony, something completely different for her and something she would hate and be embarrassed by happening ^^

Hmm, how about anyone into a Zebra? I can't really think of any characters in particular that I'd want that for.

Picking three of your friends, flipping their personality and likes (favorite characters) and transforming them into their polar opposites.

(ie: Fluttershy -> Gilda, Twilight -> Trixie/Silverstream, etc.)

Batpony trips over and accidentally bites Fluttershy, who was just beginning to become Flutterbat anyways from the full moon or (Reason goes here), and now believes that he can transform ponies into bat ponies.
Daring Do gets petrified by a Medusa-Like snake pony, who transforms her into a snake pony like herself by sculpting Daring's body then unpetrifying her.
You get brought to the Mirror Pool by the last Pinkie Pie clone, who turns you into a twin of herself. Parties Ensue.
Encountering a strange casino in Vegas and down to your bottom dollar, you decide to play the slots. Your body changes every time you hit the reels, and there's no turning back without a jackpot!
While visiting a Pokemon daycare, a Ditto falls on (or more likely over) you and uses Transform! Oh look, someone else just dropped off their pokemon too!

Rainbow Dash needs to get new recruits for the wonderbolts. While searching up for idea she finds the spell that makes so many guards look alike. During the training in the next batch of recruits that come in she uses this training book. Of course it's cursed and she makes everyone exactly like her.

make the pretty mare

Some dude to Queen Chrysalis