There have been many ways that people use standards for fluorescence but the one big one that has been used in flow cytometry and imaging. The one area that has developed a lot is the use of plastic fluorescent beads as controls. There are obviously many companies that have developed that but the one company that has developed many beads in this area is called spherotech.
Usin’Life scientists use these beads (pdf here) to set up their controls and standards. This helps in standardizing the instrumentation but also makes them comparable with other companies and customers.
The bead technology has developed substantially, such that now beads come pre-labeled with fluorescent tags of different varieties and they can be managed easily, without worrying about photobleaching, or other complications.