Although the literature on control of overhead crane systems is extensive and relatively mature, there is still a need to develop strategies that can simultaneously handle factors such as the double pendulum effect, variable cable length, input saturation, input dead zones, and external disturbances. This article is concerned with adaptive tracking control for underactuated overhead cranes in the presence of the above-mentioned challenging effects. The proposed controller is composed of the following two components. First, a tracking signal vector that effectively reduces system swing magnitudes is constructed to improve the transient performance and guarantee smooth operation of the system. Second, an adaptive law is designed to estimate and compensate for the overall effects of the friction, the external disturbances, and certain nonlinearities. The system stability has been proved rigorously via the Lyapunov method and Barbalat's lemma. Extensions to the cases with input saturation and dead zones have also been discussed. Extensive numerical simulations have been conducted to verify the performance and robustness of the proposed controller, in comparison to some existing methods.