While distance education in various forms has existed for many years, the exponential growth of computer-based, especially web-based, education has presented a challenge for instructors who learned to operate in a traditional classroom environment. Not only must they design engaging, effective learning modules with authentic assessments, promote interaction and gauge understanding throughout the term, they must now do so without being able to see their students and without the students’ ability to participate in typical classroom activities (Edelson, 2001). This is especially problematic for subject areas such as science and mathematics, where demonstration and experiential activities are essential. Despite these complexities, there is tremendous potential for effective, engaging science instruction through distance learning, but also a pronounced, crippling disconnect between the technology being used in other disciplines—computer modeling, for example—and instructional design. Online faculty and instructional designers typically do not collaborate with computer science colleagues who have the equipment required to design sophisticated learning modules. Such sophisticated modules would move beyond the context and resource focused modules that are common—and acceptable, while not ideal, for citizen science-level learning—to those that provide tools and scaffolds that meet the needs of all science learners. A wide range of relevant technologies exist, including games, simulations, modeling, virtual instrumentation and animation (Elgamal, Fraser & McMartin, 2005; Kin, 2004; Young-Suk, 2004). This chapter presents original research that investigates current uses of these web-based instructional technologies.