This thesis examines two aspects of the non-equilibrium dynamics of Bose-Einstein condensates (BECs). Our particular interests are the relaxation of near-integrable systems, and the inter-particle correlations present in BECs, both in equilibrium and following an abrupt change in the Hamiltonian. In the first part of this thesis we investigate the stability of solitary wave solutions to a system of two coupled one-dimensional non-linear Schrödinger equations (CNLSE). This system has an integrable point known as the Manakov[1] model which has analytic dark-bright soliton solutions[2]. We break the integrability of this model by varying the inter-species interaction strength, and employ variational and numerical methods in order to find dark-bright solitary wave solutions, away from the integrable point. The time evolution of these states is calculated via numerical integration of the CNLSE, which allows us to assess the stability of these solutions in isolation and to quantify their robustness against collisions with a dark soliton. We find that there is a broad region of the parameter space in which solutions for black-bright (stationary) solitary waves can be found. In this domain, the integrability breaking is revealed only during collisions. Prior to a collision, the numerical solutions are indistinguishable from true solitons, however, the collisional stability of these solitary waves is significantly affected by the extent to which integrability is broken. We find that there is a smooth transition between the non-dispersive particle-like nature of soliton interactions for integrable systems, and the destructive collisions which take place when the system is perturbed far from the integrable point. In the case of moving (grey-bright) solitary waves, we find a more restricted region of the parameter space which admits solitary wave solutions. In this domain we are able to find approximately stable solitary wave solutions using a variational ansatz. The collisional stability of these grey-bright solitary waves is also found to depend upon the extent to which integrability is broken. We conclude that the observation of stable, long-lived dark-bright solitary waves is not sufficient to indicate near-integrability of the two-component system. However, near-integrability may inferred if dark-bright solitary waves are observed to survive multiple collisions. These results are not only of theoretical interest, but may also inform future experiments which explore the behaviour of solitary waves in two-component Bose-Einstein condensates. Following this we investigate the properties of magnetic solitary wave solutions to the CNLSE. We find that the analytic ‘magnetic soliton’ solutions derived in reference [3] are dynamically unstable and relax to non-stationary magnetic solitary wave states over a short timescale. We investigate the collisional dynamics of these magnetic solitary waves and find that these excitations are remarkably robust. In the second part of this thesis we calculate the fluctuations in the number difference between two sub-regions of a Bose-Einstein condensate. This study is motivated by recent experiments performed by the Truscott group at the Australian National University (ANU), which indicate sub- Poissonian fluctuations even for condensates with large thermal depletion. This result cannot easily be reconciled with existing literature, which predicts strongly super-Poissonian fluctuations below the critical temperature (Tc). We develop one-dimensional, and three-dimensional, models to describe these experiments and employ the Bogoliubov formalism to explore the quantum fluctuations of the condensate, which have not previously been studied in detail. We calculate the relative number fluctuations between two halves of the condensate, and also between multiple pairs of spatial bins. For harmonically confined condensates at zero temperature, quantum correlations result in a suppression of the relative number fluctuations between the two halves of the condensate below the shot-noise level. However, the presence of even a small thermal component results in strongly super-Poissonian fluctuations below Tc; this is in agreement with the existing theoretical and experimental results. In addition, we find that the fluctuations of the harmonically confined condensate are non-uniform, with the relative number fluctuations being peaked towards the edges of the condensate. The recent studies of the Truscott group measure the fluctuations after free expansion. We therefore calculate the propagation of correlations following a sudden removal of the harmonic confinement. We find that free expansion results in a strong decrease in the relative number fluctuations. Condensates which exhibit super-Poissonian fluctuations when harmonically confined may therefore display number- squeezing after expansion. A second set of experiments by the Truscott group measured the density fluctuations present in small ‘atom laser’ pulses of atoms out-coupled from their BEC. We also model this procedure and find that immediately after the out-coupling process, the number fluctuations of the out-coupled atomic pulse are approximately Poissonian, irrespective of the correlations present in the atomic reservoir. However, the competing effects of interactions between the atomic pulse and the condensate reservoir, and free expansion of the pulse after out-coupling, can result in the measured fluctuations being either number squeezed or super-Poissonian. Our results will guide future experiments planned by the Truscott group.