The `gnome' USE flag description for Transmission is vague, and doesn't let the user know what it's actually supposed to do. Upon digging through the source code, enabling the `gnome' USE flag, which in turn enables gconf support, allows Transmission to set itself as the default URL handler for bittorrent magnet URIs. I think the Transmission's `gnome' USE flag description should be changed to reflect this.
Fixed in 2.30_beta3. I've dropped gnome USE flag completely as it's unnecessary: starting with glib-2.28 (which is stable now) magnet links should be registered with .desktop files and .desktop file in 2.30* registers itself as magnetlink handler, thus gnome USE flag (and dependency on gconf) is not necessary any more. Thank you for report!