In the aerospace field, electromechanical actuators are increasingly being implemented in place of conventional hydraulic actuators. For safety-critical embedded actuation applications like flight controls, the use of electromechanical actuators introduces specific issues related to thermal balance, reflected inertia, parasitic motion due to compliance and response to failure. Unfortunately, the physical effects governing the actuator behaviour are multidisciplinary, coupled and nonlinear. Although numerous multi-domain and system-level simulation packages are now available on the market, these effects are rarely addressed as a whole because of a lack of scientific approaches for model architecting, multi-purpose incremental modelling and judicious model implementation. In this publication, virtual prototyping of electromechanical actuators is addressed using the Bond-Graph formalism. New approaches are proposed to enable incremental modelling, thermal balance analysis, response to free-run or jamming faults, impact of compliance on parasitic motion, and influence of temperature. A special focus is placed on friction and compliance of the mechanical transmission with fault injection and temperature dependence. Aileron actuation is used to highlight the proposals for control design, energy consumption and thermal analysis, power network pollution analysis and fault response.