Every topological 3-manifold carries a smooth structure, unique up to diffeomorphism. In addition, "up to homotopy", the maps between them are the same: every continuous map is homotopic to a smooth map, and any homotopy between smooth maps is homotopic to a smooth homotopy (true for any pair of closed smooth manifolds. Probably the inclusion of mapping spaces $\text{Smooth}(M,N) \hookrightarrow \text{Cont}(M,N)$ is a homotopy equivalence, given the right topologies; all one really needs is to be able to homotope continuous maps that are smooth on the boundary to smooth maps, even if the domain is a manifold with corners.)
For closed orientable surfaces of genus $g>1$, $\text{Diffeo}(\Sigma) \hookrightarrow \text{Homeo}(\Sigma)$ is a homotopy equivalence; one can essentially see this by showing that each is homotopy equivalent to the discrete group $\text{Out}(\pi_1)$. (One can check by hand that it's a homotopy equivalence for $\Sigma = S^2$ or $T^2$; but no longer to a discrete group.)
What can we say for the same situation in closed 3-manifolds? Is the inclusion $\text{Diffeo}(M) \hookrightarrow \text{Homeo}(M)$ a homotopy equivalence? Does it at least induce a bijection on $\pi_0$ (i.e., induces an isomorphism on the smooth and continuous mapping class groups?) If not, can we restrict to some subclass (hyperbolic?) for which either of these is true?
(By the computation of mapping class groups of tori, or noting the existence of exotic spheres, this fails miserably for $n \geq 5$. Presumably it also fails miserably for $n=4$.)