Maladaptive decision-making is increasingly recognized to play a significant role in numerous psychiatric disorders, such that therapeutics capable of ameliorating core impairments in judgment may be beneficial in a range of patient populations. The field of “decision neuroscience” is therefore in its ascendancy, with researchers from diverse fields bringing their expertise to bear on this complex and fascinating problem. In addition to the advances in neuroimaging and computational neuroscience that contribute enormously to this area, an increase in the complexity and sophistication of behavioral paradigms designed for nonhuman laboratory animals has also had a significant impact on researchers' ability to test the causal nature of hypotheses pertaining to the neural circuitry underlying the choice process. Multiple such decision-making assays have been developed to investigate the neural and neurochemical bases of different types of cost/benefit decisions. However, what may seem like relatively trivial variation in behavioral methodologies can actually result in recruitment of distinct cognitive mechanisms, and alter the neurobiological processes that regulate choice. Here we focus on two areas of particular interest, namely, decisions that involve an assessment of uncertainty or effort, and compare some of the most prominent behavioral paradigms that have been used to investigate these processes in laboratory rodents. We illustrate how an appreciation of the diversity in the nature of these tasks can lead to important insights into the circumstances under which different neural regions make critical contributions to decision making.