Let $M$ be a closed, orientable, irreducible, geometrizable 3-manifold. We prove that the profinite topology on the fundamental group of $pi_1(M)$ is efficient with respect to the JSJ decomposition of $M$. We go on to prove that $pi_1(M)$ is good, in
the sense of Serre, if all the pieces of the JSJ decomposition are. We also prove that if $M$ is a graph manifold then $pi_1(M)$ is conjugacy separable.
We classify those compact 3-manifolds with incompressible toral boundary whose fundamental groups are residually free. For example, if such a manifold $M$ is prime and orientable and the fundamental group of $M$ is non-trivial then $M cong Sigmatimes S^1$, where $Sigma$ is a surface.
