Embryonic development hinges on effective coordination of molecular events across space and time. Waves have recently emerged as an ubiquitous mechanism that ensure rapid spreading of regulatory signals across embryos, as well as reliable control of their patterning, namely for the emergence of body plan structures. Here, we review a selection of recent quantitative work on signaling waves, and present an overview of theory of waves. Our aim is to provide a succinct, yet comprehensive guiding reference for the theoretical frameworks by which signaling waves can arise in embryos. We start then from reaction-diffusion systems, both static and time-dependent, move to excitable dynamics and conclude with systems of coupled oscillators. We link these theoretical models to molecular mechanisms recently elucidated for the control of mitotic waves in early embryos, patterning of the vertebrate body axis, micropattern cultures and bone regeneration. Our goal is to inspire experimental work that will advance theory in development and bridge its predictions to quantitative biological observations.