Differing boundary/mixed-layer height measurement methods were assessed in moderately-polluted and clean environments, with a focus on the Vaisala CL51 ceilometer. This intercomparison was performed as part of ongoing measurements at the Chemistry And Physics of the Atmospheric Boundary Layer Experiment (CAPABLE) site in Hampton, Virginia and during the 2014 Deriving Information on Surface Conditions from Column and Vertically Resolved Observations Relevant to Air Quality (DISCOVER-AQ) field campaign that took place in and around Denver, Colorado. We analyzed CL51 data that were collected via two different methods (BLView software, which applied correction factors, and simple terminal emulation logging) to determine the impact of data collection methodology. Further, we evaluated the STRucture of the ATmosphere (STRAT) algorithm as an open-source alternative to BLView (note that the current work presents an evaluation of the BLView and STRAT algorithms and does not intend to act as a validation of either). Filtering criteria were defined according to the change in mixed-layer height (MLH) distributions for each instrument and algorithm and were applied throughout the analysis to remove high-frequency fluctuations from the MLH retrievals. Of primary interest was determining how the different data-collection methodologies and algorithms compare to each other and to radiosonde-derived boundary-layer heights when deployed as part of a larger instrument network. We determined that data-collection methodology is not as important as the processing algorithm and that much of the algorithm differences might be driven by impacts of local meteorology and precipitation events that pose algorithm difficulties. The results of this study show that a common processing algorithm is necessary for LIght Detection And Ranging (LIDAR)-based MLH intercomparisons, and ceilometer-network operation and that sonde-derived boundary layer heights are higher (10-15% at mid-day) than LIDAR-derived mixed-layer heights. We show that averaging the retrieved MLH to 1-hour resolution (an appropriate time scale for a priori data model initialization) significantly improved correlation between differing instruments and differing algorithms.