The dark energy is one of the great mysteries of modern cosmology, responsible for the current acceleration of the expansion of our Universe. Its study is a major focus of my thesis : the way I choose to do so is based on the large-scale structure of the Universe, through a probe called the integrated Sachs-Wolfe effect (iSW). This effect is theoretically detectable in the cosmic microwave background (CMB) : before reaching us this light travelled through large structures underlain by gravitational potentials. The acceleration of the expansion stretches and flattens these potentials during the crossing of photons, changing their energy, in a way that depend on the properties of the dark energy. The iSW effect only has a weak effect on the CMB requiring the use of external data to be detectable. A conventional approach is to correlate the CMB with a tracer of the distribution of matter, and therefore the underlying potentials. This has been attempted numerous times with galaxies surveys but the measured correlation has yet to give a definitive result on the detection of the iSW effect. This is mainly due to the shortcomings of current surveys that are not deep enough and/or have a too low sky coverage. A part of my thesis is devoted to the correlation of FDC with another diffuse background, namely the cosmological infrared background (CIB), which is composed of the integrated emission of the non-resolved distant galaxies. I was able to show that it is an excellent tracer, free from the shortcomings of current surveys. The levels of significance for the expected correlation CIB-CMB exceed those of current surveys, and compete with those predicted for the future generation of very large surveys. In the following, my thesis was focused on the individual imprint in the CMB of the largest structures by iSW effect. My work on the subject first involved revisiting a past study of stacking CMB patches at structures location, using my own protocol, completed and associated with a variety of statistical tests to check the significance of these results. This point proved to be particularly difficult to assess and subject to possible selection bias. I extended the use of this detection method to other available catalogues of structures, more consequent and supposedly more sophisticated in their detection algorithms. The results from one of them suggests the presence of a signal at scales and amplitude consistent with the theory, but with moderate significance. The stacking results raise questions regarding the expected signal : this led me to work on a theoretical prediction of the iSW effect produced by structures, through simulations based on the Lemaître-Tolman-Bondi metric. This allowed me to predict the exact theoretical iSW effect of existing structures. The central amplitude of the measured signals is consistent with the theory, but shows features non-reproducible by my predictions. An extension to the additional catalogues will verify the significance of their signals and their compatibility with the theory. Another part of my thesis focuses on a distant time in the history of the Universe, called reionisation : the transition from a neutral universe to a fully ionised one under the action of the first stars and other ionising sources. This period has a significant influence on the CMB and its statistical properties, in particular the power spectrum of its polarisation fluctuations. In my case, I focused on the use of temperature measurements of the intergalactic medium during the reionisation in order to investigate the possible contribution of the disintegration and annihilation of the hypothetical dark matter. Starting from a theoretical work based on several models of dark matter, I computed and compared predictions to actual measures of the IGM temperature, which allowed me to extract new and interesting constraints on the critical parameters of the dark matter and crucial features of the reionisation itself