While there is a consensus in the literature that embracing nanodevices and nanomaterials helps in improving the efficiency and performance, the reason for the better performance is mostly subscribed to the nanosized material/structure of the system without sufficiently acknowledging the role of fluid flow mechanisms in these systems. This is evident from the literature review of fluid flow modeling in various energy-related applications, which reveals that the fundamental understanding of fluid transport at micro- and nanoscale is not adequately adapted in models. Incomplete or insufficient physics for the fluid flow can lead to untapped potential of these applications that can be used to increase their performance. This paper reviews the current state of research for the physics of gas and liquid flow at micro- and nanoscale and identified critical gaps to improve fluid flow modeling in four different applications related to the energy sector. The review for gas flow focuses on fundamentals of gas flow at rarefied conditions, the velocity slip, and temperature jump conditions. The review for liquid flow provides fundamental flow regimes of liquid flow, and liquid slip models as a function of key modeling parameters. The four porous media applications from energy sector considered in this review are (i) electrokinetic energy conversion devices, (ii) membrane-based water desalination through reverse osmosis, (iii) shale reservoirs, and (iv) hydrogen storage, respectively. Review of fluid flow modeling literature from these applications reveals that further improvements can be made by (i) modeling slip length as a function of key parameters, (ii) coupling the dependency of wettability and slip, (iii) using a reservoir-on-chip approach that can enable capturing the subcontinuum effects contributing to fluid flow in shale reservoirs, and (iv) including Knudsen diffusion and slip in the governing equations of hydrogen gas storage.