Hydrogels are widely used to produce biomolecular separations in electrophoretic applications, where gel morphology and charge effects combine to produce the separation. Nanocomposite gels are poised to revolutionize this field in both improved handling characteristics and improved separations. Gel morphology and charge effects have traditionally been manipulated by varying the copolymer composition, but recent reports show that novel morphological changes can also be induced in the gel using templating methods and nanoparticle additton. To aid realization of the potential for novel electrically driven separations arising from such novel morphologies, we review here advances in materials development alongside a review of the directions in biomolecule/hydrogel electrophoretic transport modeling. Models for polyelectrolyte transport that are potentially useful for understanding novel behaviors caused by gel morphology are analyzed first. With the perspective of theoretical guidance, we then survey nanocomposite hydrogel morphologies keyed by the nanoparticle and matrix. Finally, we survey as well reports of dramatic improvements in the mechanical properties that may be the key to the early adoption of these new materials in biomolecular separation applications. For modeling, we have identified the different scales involved in biomolecular transport in these materials and provided a taxonomy of transport models that emphasize the role of gel morphology in determining both polyelectrolyte mobility and diffusion. Three aspects for future work unique to nanocomposite gel materials are described: (a) descriptions of the distribution of nanoparticles within the gels; (b) descriptions of the motion of the buffer solution that may include electroosmotic effects for nanoparticles with surface charges; (c) descriptions of the motion of the polyelectrolyte molecule inside the new gel material for a given application. These aspects will help to uncover further quantitative details about the ability of these gels to be tunable for differential mass transport of a given type of molecule. Standard gels, currently, lack a broad flexibility to increase the separation of biomolecules and, in general, are not tunable.