Not all eye-tracking methodology and data processing are equal. While the use of eye-tracking is intricate because of its grounding in visual physiology, traditional 2D eye-tracking methods are supported by software, tools, and reference studies. This is not so true for eye-tracking methods applied in virtual reality (imaginary 3D environments). Previous research regarded the domain of eye-tracking in 3D virtual reality as an untamed realm with unaddressed issues. The present paper explores these issues, discusses possible solutions at a theoretical level, and offers example implementations. The paper also proposes a workflow and software architecture that encompasses an entire experimental scenario, including virtual scene preparation and operationalization of visual stimuli, experimental data collection and considerations for ambiguous visual stimuli, post-hoc data correction, data aggregation, and visualization. The paper is accompanied by examples of eye-tracking data collection and evaluation based on ongoing research of indoor evacuation behavior.