(1) The older and more widely known applications are to regularity and solvability of PDEs of any order that are not necessarily elliptic.
(2) The phenomenon of the propagation of singularities along certain submanifolds of the cotangent space is also another striking application.
These refined notions of hypoellipticity and solvability as well as the propagation of singularities involve many fantastic results which are possible because of microlocal analysis. Even the statements of many of these results require microlocal analysis.
(3) There are also several applications to several complex variables and a very active subfield called CR (for Cauchy Riemann) manifolds.
Some of the standard references on these topics are the two volumes of F. Treves on Introduction to Pseudodifferential and Fourier Integral Operators and the L. Hormander's treatise (Volumes I, II, III, etc).