Thermally driven microfluidics, that is, flow that is driven by a temperature gradient, has applications from lab-on-a-chip to electronics cooling. Development of such devices requires tools to predict and probe temperature and velocity fields. We have developed analytical, numerical, and experimental analysis tools for design and characterization of thermally driven microfluidic systems. We demonstrate these tools through the analysis of two different systems: an electrothermal microstirring biochip, and a high aspect heat pipe for cooling. First, a numerical model is developed for temperature and velocity fields, in a hybrid electrothermal-buoyancy microstirring device. An analytical tool, the electrothermal Rayleigh number, is used to further explore the relative importance of electrothermal and buoyancy driven flow. Finally, two experimental thermometry techniques are described: fluorescence thermometry and infrared thermometry. These analytical, numerical, and experimental tools are useful in the design of thermally driven microfluidic systems, as demonstrated here through the development and analysis of microstirring and heat pipe systems.