I'd say Brinkmanship
was my favourite of the Typhon Pact books, doing the best work with the Tzenkethi and the characterisation on the Enterprise.
I'd say Rough Beasts
, Plagues of Night
and Raise the Dawn
are really good too, with a great arc, and the latter two also serving as a capstone for the series (except for Brinkmanship which is the chronological latest part of the series?).
Paths of Disharmony
was my least favourite of the ones I read (I never read the Titan ones nor the eshort about the Kinshaya).