Temperatures of the lower crust and Moho are critical boundary conditions for models of heat transfer and production in the lithosphere, as well as models of the bulk composition of the continental crust, yet they remain uncertain. This dissertation focuses on xenoliths—fragments of in situ deep crust transported rapidly to the surface by volcanism—and accessory phase U-Pb and trace-element petrochronology in order to provide direct insights into the long-term thermal history of lower continental crust. Chapter I constitutes a study of xenoliths and basement outcrops from northern Tanzania aimed at unraveling crustal vs. mantle heat contributions to variable surface heat flow across the tectonically-stable craton and adjacent rifting crust. Lower-crustal xenoliths erupted on the craton edge contain rutile with U-Pb dates as old as 1000 Ma, whereas xenoliths from the rift have rutile and apatite with near-zero Ma U-Pb dates but significantly older titanite dates (up to 560 Ma). These and other data suggest that Moho temperatures beneath the craton margin are cooler than below the rifting crust, such that regional differences in surface heat flow reflect variable mantle heat flow. Chapter II focuses on kimberlite-borne xenoliths from the central Siberian craton. Rutile and apatite in garnet-granulite xenoliths preserve U-Pb dates between 1.8 Ga and 360 Ma (the timing of kimberlite eruption). Such spreads in U-Pb dates have been interpreted previously to reflect partial Pb loss during slow cooling through the Pb closure temperatures of rutile/apatite, but could also result from brief heating pulses in the lower crust prior to eruption. Laser ablation depth profiling reveals that U-Pb age and elemental gradients in rutile are coupled, contrary to diffusive decoupling expected for thermally-mediated volume diffusion over billions of years. These data are instead best explained by multiple transient heating episodes during distinct thermotectonic events, including immediately prior to kimberlite eruption. Finally, Chapter III presents TIMS and LASS-ICP-MS data for potential reference apatites. Using microbeam methods to obtain precise and accurate U-Pb, Sm-Nd, Sr isotopes and elemental abundances from apatite—a petrologically diverse thermochronometer—requires well-characterized and matrix-matched reference materials, yet suitable reference apatites are scarce. The development of the reference apatite suite provides new benchmarks for in situ apatite isotopic analyses and inter-laboratory calibrations.