The self-assembly of functional ordered structures from discrete building blocks is a central process in nanotechnology. The building blocks giving rise to organised nanometre- and micron-size materials span a wide range of technologically important substances, including amphiphilic molecules, nanocrystals and many other organic and inorganic molecules. While in the past few decades we have witnessed significant advances in synthesis and assembly technologies, achieving architecture designability remains an important challenge. This task requires a detailed insight into the relevant length- and time-scales at which thermal agitation and fluctuations on such particles occur. Statistical mechanics is the theoretical framework defining the equilibrium and out-of equilibrium properties of these many-body systems; computer simulations of particle-based models are the tools that make their investigation possible. This thesis is primarily devoted to the study of relevant self-assembling soft-matter systems by computer simulation. The first part is dedicated to the derivation of coarse-grained potentials describing effective interactions of Methacrylate-based block-copolymers, which have been recognised as excellent candidates for the assembly of nano-structured aggregates. The examination of the aggregation behaviour of low-molecular weight poly(ethylene oxide-b-butylmethacrylate) copolymers reveals a set of morphologies that can be controlled solely by the ratio of selective and common solvents. Morphological phase diagrams are presented and the effects of solvent correlations and chain conformation on the morphological transitions of self-assembled aggregates are investigated. This thesis also addresses the assembly the ionic surfactant Cetyl Trimethyl Ammonium Bromide and an OH-terminated propa(ethylene glycol) alkanethiol surfactant onto the surface of gold nanorods. The stabilised structures, including hemimicelles, cylindrical micelles and bilayers, show a strong dependence on the relative surfactant composition and the in-plane order of adsorbed headgroups. A systematic study of the phase-behaviour of rod-like nanocrystals coated with a soft repulsive corona demonstrates that the ubiquitous hexagonal close-packing observed in assembled superlattices of standing aligned colloidal rods is not the only accessible symmetry. Depending on the macroscopic conditions, other non-conventional phases such as square crystals can be assembled. This curious behaviour may lead to new ways for controlling the assembly of anisotropic nanoparticles into structures with pre-engineered catalytic and optical properties. Finally we study how the introduction of geometric constraints in confined glass-former glycerol induces molecular ordering close to symmetry breaking and the important implications on its dynamics.