This paper presents an overview and discusses the role of certification in safety-critical computer systems focusing on software, and partially hardware, used in the civil aviation domain. It discusses certification activities according to RTCA DO-178B "Software Considerations in Airborne Systems and Equipment Certification" and touches on tool qualification according to RTCA DO-254 "Design Assurance Guidance for Airborne Electronic Hardware." Specifically, certification issues as related to real-time operating systems and programming languages are reviewed, as well as software development tools and complex electronic hardware tool qualification processes are discussed. Results of an independent industry survey done by the authors are also presented.