Nanoscale devices, also called nanomachines, form communication networks and cooperate with each other so that they can be used to perform complicated tasks. Such networks of nanodevices, named nanonetworks, envisioned to serve the functionality and performance of today's Internet. This paper presents a comparative review of the state-of-the-art electromagnetic (EM) nanonetworks highlighting their potentials and challenges in a comprehensive manner. We first introduce the promising areas of applications of nanonetworks; therein, we explain how it can be useful in biomedical fields, environmental domains, consumer products, military systems, and on-chip wireless communications. Then, the survey focuses on the basic principles of fundamental physical layer issues enabling nanonetworks; the discussion includes frequency bands, modulation and demodulation, and EM properties of nanoparticles. Subsequently, the study provides an overview of transmission characteristics including channels, channel coding, and energy constraint nature of nanonetworks. Furthermore, we provide an in-depth discussion on nanoantenna highlighting its variants and their characteristics; give an overview of network layer issues; and discuss the security issues in EM nanonetworks. The study argues that despite the significant recent development of EM communication as one of the most desired modes of nano communications, the limited capabilities of nanomachines introduce a new set of challenges and unique requirements and pose unseen characteristics that need to be deliberately addressed. On that, the review finally provides a critical discussion on the applicability of EM mode for nano communication networks highlighting the future challenges with a set of perspectives of possible solutions.