Two words:
Mr. Mime
His legs and hands flash.
Some of Giratina Origin's tentacle-ribbony things flash:
Also, one of his horns has a white spot appear in it on some frames.
Flashing stingers on Beedrill, also, oddly colored wings:
The feather on Blaziken-M's leg flashes white:
Sealeo (lol) has flashing eyes:
The whites of Shinx's eyes are blue instead of white:
The outline of Spiritomb's eyes flash white:
Chesnaught's shell flashes
BAAAD flickering on Cobalion's legs
Mega Venusaur's tree's trunk flashes
Doublade's blades flash