System identification methods have played an essential role in the research and industry projects at the Institute of Flight System Dynamics of the Technical University of Munich. Besides the application of the established system identification approaches to multiple aircraft, novel methods have been developed at the institute to deal with the challenges associated with fixed- and rotary-wing aircraft system identification in the time and frequency domains. This paper provides an overview of these new developments, as well as practical application examples from the past and ongoing projects at the institute. After a brief introduction to the work at the institute, the paper describes the new advancements in the fields of time domain system identification and optimal input design by introducing optimal control methods. It continues with an alternative problem formulation for applying frequency domain system identification and parameter estimation methods to a novel flight control design and tuning approach. Additional topics from the past and ongoing research at the institute such as novel methods and practical findings in rotorcraft system identification and flight path reconstruction for different applications will be discussed and referenced.