1. The sand trail in Ash Lake leading to the Everlasting Dragon is significantly wider. I remember patching to 1.05 and it was very narrow.
2. The Living Tree that blocks the side path in Darkroot Garden leading to the Moonlight Fluttershy (oh shi-) now has a gap to the right of it, meaning you don't have to kill the tree to enter the path.
3. The machine that shoots boulders in Sen's Fortress now shoots 2 boulders in series per firing. I think this one is a glitch.
I've seen other changes but can't remember right now.