After installing media-gfx/rawtherapee "xdg-open ~" launches it, instead of nautilus (I have gnome 3.2). rawtherapee's bundled .desktop file has inode/directory as a supported mime, and developers said that it's intentional (http://code.google.com/p/rawtherapee/issues/detail?id=1398), but still, it's not the best idea to make it the default file browser.
Fixed in 4.0.9-r1.