Photonic crystal waveguides (PhCWG) with intentional defects and unavoidable disorder exhibit high quality factor (Q) resonances. Single- and multi-resonance systems based on them are suitable for applications such as optical memories, delay lines and cavity QED. Therefore, characterization, control and investigation of the optical properties of these resonances will pave the way to their applications. The aim of this thesis is to provide theories and models to explain the transmission, reflection and dispersion spectra of these resonances, and to develop experimental methods to probe and control these resonances. The theoretical investigation in this thesis explore methods of calculating the key parameter coupling factor which determines the dispersion of a multi-resonance system. In the theoretical study, the physical cause of the pronounced asymmetric dispersion of a multi-resonance system base on mode-gap cavities is uncovered, and a dispersive mode coupling model that accurately describes the asymmetric dispersion is formulated. Experimental and theoretical investigations of reflection and transmission spectra of resonances in PhCWGs are performed. Fano lineshapes in reflection spectra are characterized experimentally, and their origin is uncovered by an accurate analytical model proposed in this thesis. A simple scheme of manipulating the Fano lineshape proposed from our model is demonstrated experimentally. The abnormally high transmission TM (transverse magnetic)-like light signal has been measured and analyzed in this thesis. From our analysis, we conclude that TE (transverse electric)/TM conversion is a substantial channel for cavity losses. A new non-invasive method to elucidate the spatial profile of the localized modes in a photonic crystal waveguide with unavoidable disorder using precise local thermal tuning is proposed. Using this method, the spatial profile of a localized mode with Q > 105 with a resolution of 2.5 μm is successfully reconstructed. Furthermore, the hybridization of two disorder-induced resonances is shown and the mode profiles of the hybridized modes are reconstructed. Finally, the experimental result of one order of magnitude increase of the Q of a disorder-induced resonance is shown.