Ninux, in Italia, uses a mix of B.A.T.M.A.N., OLSR, BGP, GRE, and VPN. The complete architecture is described in great depth in this document (original source at Google docs)
HamWAN
HamWAN is an amateur radio data network near Seattle.
K-Net, in Denmark is an internet access provider that started in 1996 as a network between 3 dormitories and have since evolved to a full featured ISP. Currently there are approximately 2500 end users sharing a 10GE link.