net-im/pidgin has an IUSE/RDEPEND named bonjour. This pulls in avahi. I didn't notice any other package using a "bonjour" flag, they are all named "zeroconf". Moreover avahi is a specific implementation (the others are mDNSResponder and howl). The USE-flag should perhaps be named "zeroconf" or "avahi". On the other hand it enables the bonjour protocol instant messaging and that is what the user might look for. Just wanted to let you know that I tripped over this while enabling zeroconf with avahi system-wide. Perhaps it's worth discussing or there is even a technical solution for this.
bonjour is the IM protocol... avahi/zeroconf are implementation details
