At a guess, that would probably require rewriting (to use your example) Gaim's code, as well as the code of each other application you'd like to alter. There are some applications that will make themselves transparent/translucent, like wterm, but afaik it's an application-specific addition, not a windowmanager-wide thing.
There appears to be a desktop environment that supports what they call "Selective translucency", but if that means what you want it to mean I couldn't say... It might be worth checking out?
http://freshmeat.net/projects/athene...ease_id=128268
I've got to say, though...it's a really neat idea!