The use of IP in near space is likely to work reasonably well. However for interplanetary operation, a new suite of protocols has been developed that can be layered on top of tcp/ip or can work in parallel where necessary. RFC 4838 has recently been issued to describe these new protocols. While TCP/IP should work perfectly well in near Earth orbit, in space craft, and on the surface of other planets and moons, bridging the interplanetary distances and dealing with celestial motions (e.g. planetary rotation) has required some new architectural choices.
He points to a paper he co-authored with others from NASA, Intel, MITRE and Sparta - Delay-Tolerant Networking Architecture:
In a sense, the DTN architecture provides a common method for interconnecting heterogeneous gateways or proxies that employ store-and-forward message routing to overcome communication disruptions. It provides services similar to electronic mail, but with enhanced naming, routing, and security capabilities. Nodes unable to support the full capabilities required by this architecture may be supported by application layer proxies acting as DTN applications.