I've just finished a long and painful redesign of my water layout. I'd grown to hate the way the old one looked, with the dropdowns and the messy expanding items along the left.
I toiled long and hard to get the transparency just right in Internet Explorer, which I hate even more as a developer than I do as a user. In the end, I had to sacrifice normal scrollbars in order to get the transparency just right, but I'm happy with the way it looks.
The problem comes because of the way Explorer implements transparency, via their filter effects. There are some really neat effects which don't see more use only because they're Explorer-specific. But you have to declare specific height and width in order for the filter to work. In the end, I somehow managed to persuade IE to go transparent while leaving the body height fluid, but I lost the scrollbars in doing so. Oh well, I'll take it.