Most commercial heterogeneous catalysts employ bifunctional components of active nanoparticles and high surface area supports because of the ease of product separation and catalyst recycling. The size, shape, surface structure, and dispersity of the active nanoparticles in catalysts strongly affect the common reactions. Being small in size increases the nanoparticle surface tension and makes surface atoms very active. Herein, we have synthesized uniform and small nanoparticles of Co, Ni, $Mo/MoO_x$, $MoO_3$ and $MoS_2$ and then incorporated them into MCF (mesocellular siliceous foam) structures by sonication making bifunctional catalysts. In particular, polycrystalline $Mo/MoO_x$ nanoflakes were synthesized by thermal decomposition of $Mo(CO)_6$, and easily transformed to small $MoO_3$ and $MoS_2$ nanoparticles by either oxygen bubbling or sulfur addition, respectively. To the best of our knowledge, there were no generic synthetic schemes for Ku $MoO_3$ and $MoS_2$ nanostructures as colloidal forms. It is anticipated that the colloidal forms of smaller and regular molybdenum oxides and sulfides would exhibit better catalytic performances compared to the bulk catalysts due to their large surface area and high activity. We have also applied cobalt and nickel bifunctional catalysts in Pauson-Khand and desulfurization reactions, respectively.