The recent introduction of high-resolution molecular imaging technology is considered by many experts as a major breakthrough that will potentially lead to a revolutionary paradigm shift in health care and revolutionize clinical practice. This paper intends to balance the capabilities of the two major molecular imaging modalities used in nuclear medicine, namely positron emission tomography (PET) and single photon emission computed tomography (SPECT). The motivations are many-fold: (1) to gain a better understanding of the strengths and limitations of the two imaging modalities in the context of recent and ongoing developments in hardware and software design; (2) to emphasize that certain issues, historically and commonly thought as limitations of one technology, may now instead be viewed as challenges that can be addressed; (3) to point out that current state of the art PET and SPECT scanners can (greatly) benefit from improvements in innovative image reconstruction algorithms; and (4) to identify important areas of research in PET and SPECT imaging that will be instrumental to further improvements in the two modalities. Both technologies are poised to advance molecular imaging and have a direct impact on clinical and research practice to influence the future of molecular medicine.