Graphics processing units (GPUs) offer significant speedups over CPUs for certain classes of applications. However, programming for GPUs is challenging. There are many parameters that affect performance and their values may change depending on both problem instance and GPU hardware specifics. In addition, most GPU kernels are compiled once; performance optimizations are applied at application compile time. As a result, many GPU libraries and programs have limited adaptability to variations among problem instances and hardware configurations. These factors limit code reuse and the applicability of GPU computing to a wider variety of problems. This paper introduces GPGPU kernel specialization, a technique used to describe highly adaptable kernels that exhibit high performance across a wide range of programmer variables as well as different generations of GPUs. We also introduce our GPU Prototyping Framework (GPU-PF) for dynamic runtime generation of customized GPU kernels incorporating both problem and implementation-specific parameters. GPU-PF fully separates the GPU and CPU code so the GPU code can be compiled during program execution once all the parameters are known. This work explores the implementation and parameterization of two real world applications targeting two generations of NVIDIA CUDA-enabled GPUs using kernel specialization and GPU-PF: large template matching and cone-beam image reconstruction via backprojection. Starting with high performance GPU kernels that compare favorably to multi-threaded reference implementations, kernel specialization is shown to increase adaptability while providing performance improvements including improved run time and reduction in resource usage. Kernel specialization offers productivity benefits, improved library code, and a means to increase the parameterizability of GPGPU implementations.