Emerging Monolithic Three-Dimensional (M3D) integration technology will not only provide improved circuit density through the high-bandwidth coupling of multiple vertically-stacked layers, but it can also provide new architectural opportunities for on-chip computation, memory, and communication that are beyond the capabilities of existing process and packaging technologies. For example, with massive parallel communication between heterogeneous memory and compute layers, existing processing-in-memory architectures can be optimized and expanded, developing into efficient and flexible near-data processors. Additionally, multiple tiers of interconnect can be dynamically leveraged to provide an efficient, scalable interconnect fabric that spans the three-dimensional system. This work explores some of the challenges and opportunities presented by M3D technology for emerging computer architectures, with focus on improving efficiency and increasing system flexibility.