Cloud application marketplaces of modern cloud infrastructures offer a new software deployment model, integrated with the cloud environment in its configuration and policies. However, similar to traditional software distribution which has been suffering from software piracy and reverse engineering, cloud marketplaces face the same challenges that can deter the success of the evolving ecosystem of cloud software. We present a novel system named CAFE for cloud infrastructures where sensitive software logic can be executed with high secrecy protected from any piracy or reverse engineering attempts in a virtual machine even when its operating system kernel is compromised. The key mechanism is the end-to-end framework for the execution of applications, which consists of the secure encryption and distribution of confidential application binary files, and the runtime techniques to load, decrypt, and protect the program logic by isolating them from tenant virtual machines based on hypervisor-level techniques. We evaluate applications in several software categories which are commonly offered in cloud marketplaces showing that strong confidential execution can be provided with only marginal changes (around 100-220 lines of code) and minimal performance overhead. The results demonstrate the effectiveness and practicality of CAFE in cloud marketplaces.