Recently, low molecular-weight organogel (LMOG) systems have drawn much attention not only as new functional soft-materials but also as well-defined nano-structured assemblies. In this review, molecular design and application of the second generation of LMOG are described. Firstly, stimuli-responsive organogel systems are developed. They change their molecular structure by photo- and redox-stimuli, and subsequently, their aggregation modes are controlled (sol-gel phase transition). Secondly, fluorescent organogel systems are introduced. In the organogel systems where functional dye molecules stack precisely, an unusual electron overlapping mode and an efficient energy transfer system are constructed. Thirdly, well-defined nano-structured assemblies thus designed are applied to composite materials with functional molecules, inorganic substances, and conductive polymers. By the combination of their advantages, new functional composite materials are obtained. These new findings and approaches have led us to new fields of materials chemistry and nano-chemistry.