What are the different kinds of bioluminescent genes? I know of the common green glow gene but I forgot the name and I also know that some algae glow blue. There are so many types of bioluminesent organisms, so I am wondering what species have which genes and what other genes are associated with their metabolism and the systems that regulate these genes.
There are three processes wherein light is emitted.


Bioluminescence: a chemical reaction releases light. The enzyme that does this is luciferase, while its substrate is luciferin, a small molecule. There are half a dozen organisms that have analogous (evolved independently) enzymes and totally different substrates, such as fireflies, Alivibrio bacteria, diatomes, deep sea fish, some mushrooms etc. The wiki article has a list of these and their small molecules.
Fluorescence: light is absorbed by the molecule and is emitted at a lower energy (wider wavelength, redshifted). Green fluorescent protein of Aequorea victoria jellyfish is the classic example of this. It is excited with UV and emits green light. Here is an interactive model, I threw together. Variants exists for biotech reasons that span the whole of the visible spectrum. Other species have a homologous beta barrel, such as corals (red).
Phosphorescence: light is absorbed by the molecule and emitted later.  Ignoring the picosecond delay in fluorescent small molecules (cf. fluorescent lifetime microscopy), this is exclusively a properties of lanthanide elements (e.g. Europium). Lathanide binding domains have been designed, but do no exist in nature.