The formation of clusters or specifically ordered structures is common to many materials. We will focus on some example systems where simulations are able to help elucidate ordering mechanisms. First, we will discuss the origins of particle clustering in polymer-nanoparticle composites with highly symmetric nanoparticles. Our simulations emphasize the importance of effective long-ranged polymer mediated interactions between nanoparticles that promote particle clustering without the intervention of phase separation. Next we discuss how a recent model for assembly of DNA-dendrimer molecules can be adapted to mimic the behavior of DNA-coated colloids that cluster due to "linker" DNA that selectively binds the colloids. In this case, the concentration of linker DNA controls the number of bonds that a particle can form, thereby offering the possibility to form clusters with a low coordination that inhibits phase separation. Lastly, we will discuss how the interactions between patchy colloidal particles can be modified to promoted the formation of gel structures on heating.