Despite being a Navy guy, I have accounts on Army Knowledge Online both on NIPR and SIPR and have found it easy to set up a community of interest to work classified and unclassified projects requiring collaboration between small groups.

This is the best solution I have found on SIPR for such things. The same family of sites includes Joint Knowledge Online and Defense Knowledge Online communities. If you have access to SIPRnet, you can qualify for an account under one of those umbrellas.

The other non-classified collaboration site I have used, and is currently being explored for FHA/DR coordination between US agancies, NGOs, and participating parnter countries is www.harmonieweb.org