The synthesis of nanoporous graphene by a convenient carbon nanofiber assisted self-assembly approach is reported. Porous structures with large pore volumes, high surface areas, and well-controlled pore sizes were achieved by employing spherical silica as hard templates with different diameters. Through a general wet-immersion method, transition-metal oxide (Fe3O4, Co3O4, NiO) nanocrystals can be easily loaded into nanoporous graphene papers to form three-dimensional flexible nanoarchitectures. When directly applied as electrodes in lithium-ion batteries and supercapacitors, the materials exhibited superior electrochemical performances, including an ultra-high specific capacity, an extended long cycle life, and a high rate capability. In particular, nanoporous Fe3O4-graphene composites can deliver a reversible specific capacity of 1427.5 mAh-g-1 at a high current density of 1000 mA-g-1 as anode materials in lithium-ion batteries. Furthermore, nanoporous Co3O4 graphene composites achieved a high supercapacitance of 424.2 F-g-1. This work demonstrated that the as-developed freestanding nanoporous graphene papers could have significant potential for energy storage and conversion applications.