We present ways of counting configurations of uni-trivalent Feynman graphs in 3-manifolds in order to produce invariants of these 3-manifolds and of their links, following Gauss, Witten, Bar-Natan, Kontsevich and others. We first review the construction of the simplest invariants that can be obtained in our setting. These invariants are the linking number and the Casson invariant of integer homology 3-spheres. Next we see how the involved ingredients, which may be explicitly described using gradient flows of Morse functions, allow us to define a functor on the category of framed tangles in rational homology cylinders. Finally, we describe some properties of our functor, which generalizes both a universal Vassiliev invariant for links in the ambient space and a universal finite type invariant of rational homology 3-spheres.