One of the criticisms sometimes leveled at Second Life is the proprietary nature of the platform. However, for quite some time work has been progressing on an open source server, OpenSim (the client has been open source for some time now). I know of a few people using OpenSim in education (either instead of or alongside Second Life), but one of the major issues for the future of the education market might be the challenge of creating large grids of connected OpenSim servers linking together many universities.
Particular problems might be in sharing avatar details or transferring objects (while respecting permissions, rights and roles) between different servers. Interestingly, according to Linden Labs VP of Technology, this is a service that Linden Lab themselves might one day provide for the OpenSim community. As related here in a Reuters interview.