Cloud height raised to the top of the map, so clouds no longer go through buildings.
In other words, the clouds are now up in the sky, and we can't touch them. They'll always pass over our heads.
I started writing irregular Minecraft posts on my blog about a year ago. I remember how awesome it was when I finished my first tower. It had been a pain in the ass to build, what with the creepers blowing everything up, but I still remember how it felt to look down on the clouds from my tower:
In another tower I built, I had specifically sited the ceiling of my bedroom just above cloud level, so the ceiling would be periodically obscured by cloud. Of course clouds don't really behave like that, but what the hell, I liked it.
That's all in the past now, and it makes me genuinely sad. Far more sad, in fact, than I would have believed. I've always been fascinated by clouds, and I loved the notion of building such a tall tower that I could literally look down on the clouds. And now I can't any more, because... I don't even know why. I can't think of any good reasons for doing this.
For that matter, I'm not playing until the Endermen are fixed; Notch admitted it was "a horrible idea" to make them carry blocks, and I agree. Not only can they potentially destroy anything you've built, but right now, they can move bedrock. I don't feel like having constructions I've invested hours of effort in be taken apart.
For the first time, I'm totally bummed out by Minecraft. Hopefully there'll be an update soon to fix things.