The efficiency and energy density of compression ignition (diesel) engines powered by liquid fuels make them irreplaceable in many applications, and technological and regulatory changes necessitate use of new biofuels and combustion modes to realize the economic and efficiency benefits of diesel engines with reduced emissions. To address these requirements new measurement techniques -- particularly high spatial resolution, high acquisition rate, non-intrusive optical diagnostics -- together with advanced modelling are used to investigate combustion phenomena. The purpose of this research is to implement novel optical diagnostics and analysis techniques to report high-quality data to advance understanding of transient fuel sprays and combustion, and provide improved guidance to facilitate fuel screening and combustion modelling efforts. First, the largest published data-set of diesel-like injections at a single operating condition was collected and analyzed with multiple, simultaneous optical techniques -- Rainbow Schlieren Deflectometry (RSD) and OH* chemiluminescence imaging -- to quantitatively describe a reacting jet. This uniquely large data-set was collected with a constant-pressure flow chamber maintaining diesel-like conditions and flushing combustion products for a high experimental repetition rate. First-stage combustion is described with RSD for the first time, and it is demonstrated that larger data-sets than found elsewhere in literature are required to achieve statistically stationary results. Secondly, primary reference fuels are investigated using aforementioned techniques, a novel two-color pyrometry system, and newly developed analysis techniques to determine Apparent Turbulent Flame Speed (ATFS), an important combustion parameter linked closely to both fuel characteristics and localized turbulent mixing. Third, these techniques were applied to candidate biofuels identified by the Co-Optima project. To improve visualization in cyclic, turbulent combustion, a custom metric was implemented to identify a single, representative injection from each case to facilitate analysis without the over-smoothing effects of image (ensemble) averaging; this greatly improved the ability to differentiate premixed versus diffusion-dominated sooting modes of combustion. Fuel oxygenation and volatility were shown to be significant factors effecting liquid length, mixing behavior, and sooting. The last part of this research details, with a large and statistically significant data-set, the injection-to-injection variation observed by multiple diagnostics between events at identical ambient conditions. Rigorous analysis shows that these fluctuations are due solely to the stochastic nature of turbulence, necessitating the custom metric used in the previous study. That metric is then detailed, producing a new manner in which analysis of transient, turbulent, reacting jets can be accomplished for improved results and reliability.