Bill Bryson's "Troublesome Words" is an excellent book for, among other things, learning the difference between many synonyms, such as "prone," "prostrate," "recumbent" and "supine." But it can hardly be called a massive body of reference, and it deals with many other language issues. Having a reference for the differences between synonyms seems like it could be a much more effective way of understanding them than trying to tease out the differences of meaning in two possibly quite differently worded dictionary entries. Is there such a thing?
I agree with @JohnLawler but will add that good dictionaries will list not only synonyms, but etymologies which are often crucial to understanding the subtle differences between words. If you're feeling especially prescriptivist, you may want to look at anything from “Fowler's Modern English Usage” (which constructs wonderfully complex arrays of subtle word usage) to Strunk and White's “Elements of Style” (which includes a section “Words and Expressions Commonly Misused”). Note, however, that there are many guides on style and usage and no shortage of disputed points.
I can't really conceive of a reasonable way in which one could organize and present a comprehensive list of the type you describe. You seem to be suggesting that there should be some way to objectively define the difference between two synonyms beyond "trying to tease out the differences" and I'm really not sure what that would be.
Is that what the type of format you're hoping for? I don't think it really makes sense. What does make sense is reading the definitions of both words and deciding for yourself what nuances lie between them.
Also worth noting: I'm pretty sure asking for reference lists is out of scope for this site.