Hi,
No shipping Windows or Linux distribution I know of uses video card framebuffer to off-load such complex rendering. It's done 100% in software, hence why Microsoft doesn't bother to offer it, and Linux desktops are slow at it.
NVidia has its own desktop utility for Windows. It works fine. It also has a "keystone" function which allows you transform (stretch, skew, resize, etc) your "entire desktop" freely.
But until these features ship as standard in either Windows or Linux distros (think Fedora Core 5 / RHEL 5 / CentOS 5 time-frame ;-), don't expect good performance with opaque desktops where the software is doing really slow and ugly memory maps to/from the video card, over the system interconnect, etc... I.e., don't blame Linux for attempting to implement a feature in software that Microsoft won't care attempt because it has the same issues. ;->
There is a new X extension called RENDER. It comes disabled with xorg server, however once you enable the extension and install necessary user level tools, you'll have hardware accelerated (ie: true) transparent windows.
See my previous post. I've tried the setup on a gentoo installation and it works very well.
-- sukru