I would also like to hear other instances that may not have been rude, but did leave a "why would you do that"?
Two that immediately came to mind when you asked that.
Women who, despite there being 10 empty (clean, perfectly fine) other stalls, insist on coming into the one right next to you. Dang, get away. A TAD bit of pretend privacy would be nice, thank you.
And a completely empty theater. Mom and I joke about how long it's going to be before someone comes in and decides on the seat either right in front of us or right behind us. Or even right next to us. Doesn't matter where we are - it's not like we always sit in some kind of "preferred section" of the place. SERIOUSLY?! A whole empty theater, and the only spot you could find was the one on top of us?!
In the theater, to be fair, I'm fairly limited in where I can sit, especially with some screen arrangements. I tend to sit about 3/4 of the way up right in front of the projector. If I'm too close, my head will hurt. If I'm off to one side, I won't be able to follow the movie too well, I know I get distracted by things on the side of the screen. 3D movies are worse than normal ones, and my boyfriend loves them. I have a limited window of seats I can pick while still enjoying the movie.
That being said, if there's only a few other people, I do try to leave them a bit of buffer space.
On the bus thing, I don't live in a place with regular public transit, so I'm not aware of all the etiquette of it. On the few occasions I've been on it, the buses have been fairly full, so I'm left picking whatever seat I can find. But I'd never be the person to sit right next to someone on an empty bus, I have enough anxiety and space issues with strangers that it would not happen. Actually, I'd probably set my stuff on the seat next to me and take two seats until the bus started filling up and the seat was needed, just to avoid something like this. And it's reasonable, whenever I travel around a city for a day or so, I've always got a VERY FULL backpack with me, sometimes it's hard to fit it in my lap.