Essential oils are natural products which combine antimicrobial and antioxidant activity, thus providing natural protection against microbial pathogens and other undesirable agents. Among the essential oils extracted from aromatic plants, oregano (Origanum vulgare) and thyme (Thymus vulgaris) oils have been proposed for different biomedical and industrial applications. The antimicrobial mechanisms found in these essential oils have been explained on the basis of their content in natural compounds such as carvacrol, thymol, p-cymene and c-terpinene, among others. Although these two essential oils have received much attention, scientists working in the fields of biomedicine and food science, among others, are paying increasing attention to a wider variety of aromatic natural oils in an effort to identify novel and natural applications for the inhibition of microbial pathogens. Accordingly, a detailed revision of the main essential oils and their applications in biomedicine, food science and other industrial fields is presented. The review not only focuses on the main antibacterial applications reported to date, but also in the current and future developments for the inhibition of virus and fungi.