For what it's worth, you
can snap the window, you just have to drag it to the edges of the screen manually.
There's no problem with sub windows snapping via the keyboard shortcuts, though I suppose they are drawn using standard window frames as Media Center will sometimes draw them unskinned under certain conditions. (I actually think this would be a good option for skin creators to have if someone wanted to make a "native style" Windows skin)
And loosely related to that, the sub windows still maximize
underneath the taskbar.
What I actually do now rather than snapping though, is use a split pane view.
The left pane has all my zones, and the right pane has all my content. It's perfectly sized so that I can snap any other window (e.g. my browser) to the right of the screen and you can see the full video in the left half.
There are some changes I'd like to see to support this a little better, but it works pretty well for me.