An appropriate citation would be:
Joris M. Mooij et al. (2010) "libDAI 0.2.6: A free/open source C++ library for Discrete Approximate Inference", http://www.libdai.org
or in BiBTeX format:
@misc{mooij2010libdai, author = "Joris M. Mooij et al.", title = "lib{DAI} 0.2.6: A free/open source {C}++ library for {D}iscrete {A}pproximate {I}nference", howpublished = "http://www.libdai.org/", year = 2010 }
Moreover, as a personal note, I would appreciate it to be informed about any publications using libDAI at joris dot mooij at libdai dot org.