The recent advances in thin client devices and the push to transition users' desktop delivery to cloud environments will eventually transform how desktop computers are used today. The ability to measure and adapt the performance of virtual desktop environments is a major challenge for "virtual desktop cloud" service providers. In this paper, we present the "VD-Bench" toolkit that uses a novel methodology and related metrics to benchmark thin-client based virtual desktop environments in terms of scalability and reliability. We also describe how we used a VDBench instance to benchmark the performance of: (a) popular user applications (Spreadsheet Calculator, Internet Browser, Media Player, Interactive Visualization), (b) TCP/UDP based thin client protocols (RDP, RGS, PCoIP), and (c) remote user experience (interactive response times, perceived video quality), under a variety of system load and network health conditions. Our results can help service providers to mitigate over-provisioning in sizing virtual desktop resources, and guesswork in thin client protocol configurations, and thus obtain significant cost savings while simultaneously fostering satisfied customers.