Tomographic reconstruction by transmission electron microscopy is used to reveal three-dimensional nanoparticle shapes and the stacking configurations of nanoparticle ensembles. Reconstructions are generated from bright-field image tilt series, with a sample tilt range up to +/- 70 degrees, using single or dual tilt axes. We demonstrate the feasibility of this technique for the analysis of nanomaterials, using appropriate acquisition conditions. Tomography reveals both cubic and hexagonal close-packing configurations in multi-layered arrays of size-selected In nanospheres. By tomography and phase-contrast lattice imaging, we relate the three-dimensional shape of PbSe octahedral nanoparticles to the underlying crystal structure. We also confirm simple-cubic packing in multi-layers of PbSe nanocubes and see evidence that the particle shapes have cubic symmetry. The shapes of TiO(2) nanorod bundles are shown by tomographic reconstruction to resemble flattened ellipsoids.