Afloat is a killer System Preferences utility that adds a 'float on top' option and customizable transparency settings to virtually any Cocoa app in Mac OS X. Once installed (and you restart any Cocoa apps that were running), new keyboard shortcuts and a couple of options under the Window menu will offer all sorts of handy wndow management and see-through goodness. Great for those times when you have windows layered on top of each other and just need to glance at something underneath, and when you're using a bittorrnet client to download a Quake 4 demo and you're sick of it falling underneath Adium every time you switch to chat - or just for those times when you want to show off with some sexy transparency. Check out Afloat's ReadMe (PDF link) for more details.
Afloat is freeware, a Universal Binary, and available from Emanuele Vulcano's site.