In this cumulative thesis, we present our investigations on the controlled generation of nonlinear structures in Bose-Einstein condensates (BECs). In particular, our studies can be divided in three lines of research: soliton trains, soliton gases, and rogue waves. In the first set of investigations we focus on the controlled generation of soliton trains, i.e., arrays of moving solitons. The emergence of these structures is a consequence of a matter-wave interference process initialized by a box-type configuration (BTC). This initial condition allows to solve the initial value problem analytically by means of the inverse scattering transform and to obtain expressions which characterize the entities conforming the soliton trains. Our analytical derivations cover the generation of solitons trains in one- and two-component BECs, while further numerical investigations extend our results to three-component and spinor BECs. In general, it is found that the amplitude and width of the BTC directly affects the number of solitons generated, their size, and their velocity. The symmetric configuration of the resulting solitons trains can also be altered by modifying the relative phase between the regions of the BTC. In all cases, and in view of possible experimental realizations, the addition of an external harmonic potential is considered. Our results hold as long as the width of the BTC is way smaller than the size of the condensate. Additional findings include the observation of beating solitons in spinor BECs and an analytical description of the change in amplitude of oscillating dark-bright solitons in a harmonic trap. Our second focus of research deals with the experimental generation of a dense ensemble of solitons in a two-component BEC. By employing two π/2-pulses in the presence of a magnetic- field gradient we create a periodic winding pattern that dynamically evolves into an array of soliton complexes. The spacing between windings can be controlled by the duration between the pulses. Depending on the density of windings, we observed the formation of shock-waves, dark-antidark, and dark-bright solitons, as well as dynamical processes where the periodicity of the pattern triples or smooths out. In the densest ensembles, the emerging solitons undergo continuous collisions for a long period of time, preserving the overall initial features. The latter offers a path to the study of soliton gases in BECs. Last, we focus on the realization of the Peregrine soliton (PS) in BECs. The PS is a candidate to rogue waves, i.e., extreme wave events taking place at sea. The focusing nonlinearity of deep-water wave systems leads to a modulational instability considered to be the main mechanism behind the formation of such waves. To address the focusing nonlinearity avoiding undesired instabilities, we employ a highly-imbalanced weakly-immiscible two-component BEC. With this approach, the minority component presents an effective focusing nonlinearity. Its applicability is theoretically investigated by direct numerical simulations of the GPE under relevant experimental conditions. In all cases, an excellent agreement is found between the numerically obtained PS and its analytical waveform. This approach is then employed to experimentally realize the PS. In the experimental setup, an additional small attractive potential well is included to seed the formation of the PS. Numerical 1D and 3D simulations corroborate our findings. To the best of our knowledge, this is the first realization of the PS in a BEC.