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I'm looking for a resource that best surveys the anatomy and physiology of common genetic model organisms, and how their characteristics are particularly useful for biological experiments.

For example, I'm studying the eyeless Drosophila gene, but it would help to know that species' specific compound eye anatomy and normal development, so that I can weigh the pros and cons of using that particular model organism over another.

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I don't think you will find a global DB like that. You will probably need to use flybase, mousebase, dictybase, wormbase etc etc. –  terdon Jan 29 '13 at 22:55
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In the Bgee database, you can look at gene expression and anatomy of various model species, e.g. Drosophila. This doesn't give you the full anatomy, but at least an ontology of tissues and cell types.

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