Organic semiconductors have shown promise in a number of applications well-suited to their low-cost and compatibility with large-scale manufacturing methods, but much remains unknown about the self-assembly and structure that leads to high performance devices and materials. Focusing on the newest generation of solar cell and thin-film transistor materials, we investigate the self-assembly of a series of high-performance small-molecule and polymer materials. The work primarily uses transmission electron microscopy (TEM) to investigate short- and long-range crystalline order unique to each material, aspects of the morphology that are difficult to observe by any other technique. Two common themes emerge in the thin-film morphologies. First, neighboring crystallites often adopt a preferred epitaxial arrangement known as a quadrite. Such an interface is intimately related to the details of the molecular structure; their presence is expected to be beneficial to the transport properties by increasing the connectivity on the nano-scale and allowing dead-ends, defects and grain-boundaries to be bypassed efficiently. Second, a portion of the film is found to possess micron-scale orientational order while simultaneously coexisting with a more complex nano-structure. This order can be confined to a single apparent layer similar to a liquid crystal or several overlapping layers. In addition to the TEM investigations, a new technique, polarization-dependent photoconductive atomic force microscopy was developed to investigate the consequences of micron-scale orientational order on the opto-electronic properties of a device. Overall, the results suggest that both the epitaxial and long-range order are important aspects in the best materials and that explicitly engineering self-assembly into these new materials may lead to better devices.