Fluorescent colloidal silica nanoparticles are increasingly playing important roles in the fields of biotechnology, sensing, optics and photonics. These particles have increased dye stability against photobleaching, solvents, and aggressive environments over free dye. Furthermore, in comparison to semiconductor quantum dots, they are non-toxic to living organisms and have no fluorescence intermittence. Such silica particles, referred to as Cornell dots (C dots), grown by a modified Stöber process and having covalently incorporated fluorescent dyes within them will be reported upon. New dye incorporation, varied growth chemistries, and promising architectures are important to making particles with increased versatility and applicability to the aforementioned fields. Hence, we will present new linkages for covalent incorporation of dyes into silica nanoparticles and report on size and brightness results for such chemistries and the resulting architectures that may be designed. In addition, exploratory applications in biology and photonics are under investigation.