The rapid advancement in mobile devices has illustrated the widening technological gap in health and environmental sensing. Unfortunately, the time and financial burdens imposed by the current central lab model prohibit regular sensing of crucial biological and ecological elements, which can lead to delayed responses and exacerbated conditions. Current portable diagnostic solutions lack the necessary sensitivity or multiplexing potential to address the ever-expanding library of biomarkers. An emerging solution known as surface enhanced Raman spectroscopy (SERS) can provide the sensitivity of current techniques, but with drastically improved multiplexing density. Many existing SERS applications however, require multiple processing steps to introduce samples to the enhancement surface. Practical application of SERS to diagnostics and environmental samples requires more convenient materials and methods to support the broad array of conditions in on-site sensing. In this work, three new methods to apply SERS to portable sensing systems are developed. Specifically, a new SERS diagnostic is presented that details the first implementation of SERS for real-time PCR; we accomplished multiplexed detection of MRSA genes to specifically identify species and drug resistance. Second, we developed a new flexible SERS sponge based on PDMS that provides unprecedented control over sample handling and can readily concentration organic analytes. Finally, we present a novel raster scanning protocol to address the persistent reproducibility issues that has slowed commercialization of new SERS devices. Together, these three techniques advance the development SERS as a practical and portable solution for on-site diagnostics and environmental sensing.