I am doing work in some areas that rely heavily on organic light absorption. Our projects have a very wide spectral range which creates the need for engineered molecules with absorption spectra that are somewhat tailored to our application. Therefore, understanding the molecular dynamics of the various (photopigments, chromophores, opsins, etc). I understand that there is some overlap in jargon depending on one's background, so in answering the question it may be helpful to differentiate between non-protein moieties and proteins.
Additionally, I am interested in answers from all of the taxonomic domains. The question is general in scope, but I am looking for specific classes of moieties/proteins
Maybe this part of a Dye Laser book might give you more references:
http://www.springer.com/us/book/9783540515586
It deals with the structure and properties of dyes and its influence on absorption wavelength, Stokes shift, quantum efficiency etc.
As far as proteins are concerned, the natural amino acids of which they are composed absorb only in the ultraviolet. Chromophores that are bound to the proteins can also absorb at longer wavelengths. There are many different chromophores. Heme and chlorophyll are probably the most obvious. There are also the wide range of fluorescent proteins with intrinsic visible absorbance chromophores built of amino acids, the archetype being green fluorescent protein (GFP). Some yellow proteins have covalently bound flavins.
Of particular interest to you may be the phycobilisomes (see wiki link) which are the light-harvesting protein structures of some algae and cyanobacteria and can range in absorption from blue to red depending on structure and composition.
The linked youtube video also gives some good examples of naturally occurring chromophores.
Absorption properties depend on a few major things (as others mentioned):
1) The extent of conjugation in the chromophore - typically the more conjugation (pi delocalization) the lower energy (longer wavelengths) the molecule is able to absorb
2) The rigidity of the system - especially important when talking about proteins and their absorption/emission properties
3) Solvent effects - polar vs. nonpolar and acidic vs. neutral vs. basic
https://en.wikipedia.org/wiki/Phycobilisome
https://youtu.be/c63E5yo6JCk
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