chocolate and cinnamon
The B locus (for brown) is responsible for the colors chocolate and cinnamon. These colors arise from modifications of eumelanin, the black pigment, so they are considered black-based.
The B locus has three alleles. B is associated with black pigment, and is the most dominant allele. Chocolate color, associated with the b allele, is caused by production of a brown pigment instead of black. Cinnamon is a lighter brown or reddish-brown, and is associated with the b1 allele, which is recessive to both the B and b alleles.
These colors are caused by a modification in the pathway that creates eumelanin, and therefore do not significantly affect phaeomelanin. Because the b and b1 alleles can affect spacing of melanocytes as well as the structure of eumelanin, red bb cats may appear somewhat lighter than red B- cats, but since other factors affect the color of a red cat, this is not a reliable way to tell the genotype of a red cat at the B locus.
Chocolate and cinnamon are both quite rare colors, cinnamon in particular, and are usually only found in certain breeds of cat.
brown: B locus
Black - BB, Bb, Bb1
Chocolate - bb, bb1
Cinnamon - b1b1
Remember that these colors combine with sex-linked red. Red overrides all of the black-based colors by inhibiting production of eumelanin, but tortoiseshell can combine with any of these colors to make the standard black tortoiseshell, chocolate tortoiseshell, or cinnamon tortoiseshell.
Also, it's important to remember that because black cats can only carry chocolate OR cinnamon, two black cats can have black and chocolate offspring, OR black and cinnamon offspring. The only way to get all three colors in a litter is to have one Bb1 cat and one bb1 cat.
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in-depth
Chocolate and cinnamon are on the TYRP1 (tyrosinase-related protein 1) locus. The TYRP1 enzyme converts dopachrome into eumelanin, but the variants do it slightly differently. Black eumelanin granules are round, chocolate granules are somewhat elongated, and cinnamon granules are even longer. This changes their absorption of light, which makes them different colors.
Heterozygous cats produce two variants of the protein, and therefore two variants of the eumelanin, but generally the darker one covers up the lighter one to some extent. This is a bit easier to see in their dilute versions. TYRP1 is also important to the maintenance of melanosome structure, which is why it can slightly influence red colors.
Mutations similar to chocolate occur in several other species, including dogs, cows, horses, and mice, but I have yet to find a cinnamon equivalent in other species.