The work of adhesion is an interfacial materials property that is often extracted from atomic force microscope (AFM) measurements of the pull-off force for tips in contact with flat substrates. Such measurements rely on the use of continuum contact mechanics models, which ignore the atomic structure and contain other assumptions that can be challenging to justify from experiments alone. In this work, molecular dynamics is used to examine work of adhesion values obtained from simulations that mimic such AFM experiments and to examine variables that influence the calculated work of adhesion. Ultrastrong carbon-based materials, which are relevant to high-performance AFM and nano- and micromanufacturing applications, are considered. The three tips used in the simulations were composed of amorphous carbon terminated with hydrogen (a-C H), and ultrananocrystalline diamond with and without hydrogen (UNCD-H and UNCD, respectively). The model substrate materials used were amorphous carbon with hydrogen termination (a-C-H) and without hydrogen (a-C); ultrananocrystalline diamond with (UNCD-H) and without hydrogen (UNCD); and the (111) face of single crystal diamond with (C(111)-H) and without a monolayer of hydrogen (C(111)). The a-C-H tip was found to have the lowest work of adhesion on all substrates examined, followed by the UNCD-H and then the UNCD tips. This trend is attributable to a combination of roughness on both the tip and sample, the degree of alignment of tip and substrate atoms, and the surface termination. Continuum estimates of the pull-off forces were approximately 2-5 times larger than the MD value for all but one tip-sample pair.