My company sells solutions to intercept any application playback and recording at the Windows OS level and we have a specific product targeted for Skype and other VoIP applications: http://www.nektra.com/products/audio-recorder-api/ we also sells binary instrumentation tools for companies who want to speedup their own implementation http://www.nektra.com/products/deviare-api-hook-windows/

Our technology is being used in the security field in companies such as BAE Systems stratsec, CyberPoint International, and for other uses like recording YouTube videos in http://www.jaksta.com/

Feel free to contact me, even if you just need some guidance.