This doctoral thesis presents new approaches for the characterisation of ultrafast energy flow in complex systems, based on concepts of coherent control. By initiating a photoreaction with femtosecond pulses whose temporal phase and amplitude are shaped in such a manner that specific molecular vibrations and states are addressed, the energy flow can be steered at will. The comparison between the ensuing energy flow patterns following shaped and unshaped excitation pulses constitutes a differential measurement of the function of the controlled vibrations and states within the photoreaction. Coherent control as a spectroscopic tool is first applied to biological systems, specifically the light harvesting complex LH2 from the photosynthetic purple bacterium Rhodopseudomonas acidophila, and the isolated carotenoid donor of the same complex. The pump-probe method using shaped excitation pulses is shown to be successful for the first time in controlling the natural function of a biological system, namely the flow of excitation energy in the complex network of states in LH2. By means of a closed-loop optimisation of parametrised excitations, a bending mode in the carotenoid donor can be identified as being responsible for steering the energy flow. This bu vibrational mode couples the carotenoid S2-S1 states; its frequency is determined to be 160±25cm-1. Furthermore the deactivation of the carotenoid S2 state in LH2 and in solution is studied with pump-probe and pump-deplete-probe spectroscopy. Here it is shown that there exists an alternative singlet state S*T (1Bu-) involved in the deactivation process, though only in LH2. Its function as a precursor of ultrafast triplet population and as a donor for photosynthetic energy transfer is characterised with a novel evolutionary target analysis of conventional pump-probe spectra. Secondly, coherent control as a measurement technique is applied to another extremely complex system, in this case a material dominated by non-linear interactions with instantaneous dynamics: Propagation of femtosecond pulses in optical fibres that are only a few micrometers in diameter to generate a supercontinuum of optical frequencies. Here shaped pump pulses succeed in resolving for the first time the sequential steps leading to the enormous spectral broadening. Open-loop variations of precompression allows the evolution and fission of optical solitons to be followed, while closed-loop optimisations render observable the coupling of solitons with phase-matched visible frequencies. On atoms, finally, open-loop control of interfering pathways from the ground to the excited state by application of strongly modulated spectra seeks to establish a direct link between coherent control experiments and theory. The novel phenomenon of a Fresnel zone plate in the time domain is first developed in theory and then successfully realised in experiment.