In this paper, we present a systematic approach to building useful time-dependent effective Hamiltonians in molecular quantum electrodynamics. The method is based on considering part of the system as an open quantum system and choosing a convenient unitary transformation based on the evolution operator. We illustrate our formalism by obtaining four Hamiltonians, each suitable to a different class of applications. We show that we may treat several effects of molecular quantum electrodynamics with a direct first-order perturbation theory. In addition, our effective Hamiltonians shed light on interesting physical aspects that are not explicit when employing more standard approaches. As applications, we discuss three examples: two-photon spontaneous emission, resonance energy transfer, and dispersion interactions.