Several problems in physics and engineering are modeled by reaction-advection-diffusion (RAD) equations. However, when the diffusive terms are small compared with the other ones, these problems can become difficult to solve numerically. Besides, formulating the unsteady version of these models in a semi-discrete fashion, it can be interpreted that the overall diffusivity gets smaller as the time step decreases. To overcome these drawbacks, this thesis considers the development of Galerkin (or Petrov-Galerkin) finite element methods based on approximation spaces enriched by residual-free bubbles (RFB) or multiscale functions. Beginning with the unsteady reaction-diffusion problem, new methods using multiscale functions are presented which improve the solutions in the reaction-dominated regime and/or when small time steps are adopted. They also give rise to a general concept of stabilizing unsteady problems differently along the time. In the following, it is shown that switching RFB by suitable multiscale functions in the elements connected to the outflow boundaries of the domain increases the accuracy of the solutions in this region for RAD problems with advection. Next, this methodology is further studied for systems of RAD equations. In a final contribution, an extension of the RFB method is introduced for the shallow waters equations. All these methods are tested through benchmark problems and compared with stabilized methods presenting stable and accurate results.