I can't say if this fits with every fandom discussed or if it's overly specific, but this is how I would describe the archetype dynamic I see in Holmes/Watson in addition to the other fandoms I know:
The Holmes is an unusually intelligent, sensitive character who breaks and subverts socials mores. (Usually?) pointedly romantically unattached. Highly skilled in a way that makes him very useful to society (or very dangerous). The Watson character is the wrangler, of course, the only person who really "gets" and is able to control the Holmes character, but I think there is often something queer about him as well in a really interesting way that is more subversive than the Holmes' overt queerness.
He is a for-all-appearances a well-adjusted, intelligent, social and successful person, but there's something about the Watson himself (other than the direct influence of the Holmes) that prevents him from being the perfectly socialized specimen that he at first glance seems to be. As discussed above, there is something "special" about him, but I don't think it's in a good sparkly-perfect way, but rather in the sense that there's something odd about him in addition to his sheer idyllic ordinariness. For one thing, he probably doesn't have any close friends besides the Holmes. He may try to leave the Holmes and find a more ordinary life, but he returns not because the Holmes is so dominating, but because he individually failed. He is special to the Holmes precisely because he is so perfect(ly) ordinary and conventional and yet so queer.
I actually think the Master and Doctor are a good example of this. House and Wilson, Rodney and Sheppard (sort of...), Q and Picard, Snape and Harry *g*
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The Holmes is an unusually intelligent, sensitive character who breaks and subverts socials mores. (Usually?) pointedly romantically unattached. Highly skilled in a way that makes him very useful to society (or very dangerous). The Watson character is the wrangler, of course, the only person who really "gets" and is able to control the Holmes character, but I think there is often something queer about him as well in a really interesting way that is more subversive than the Holmes' overt queerness.
He is a for-all-appearances a well-adjusted, intelligent, social and successful person, but there's something about the Watson himself (other than the direct influence of the Holmes) that prevents him from being the perfectly socialized specimen that he at first glance seems to be. As discussed above, there is something "special" about him, but I don't think it's in a good sparkly-perfect way, but rather in the sense that there's something odd about him in addition to his sheer idyllic ordinariness. For one thing, he probably doesn't have any close friends besides the Holmes. He may try to leave the Holmes and find a more ordinary life, but he returns not because the Holmes is so dominating, but because he individually failed. He is special to the Holmes precisely because he is so perfect(ly) ordinary and conventional and yet so queer.
I actually think the Master and Doctor are a good example of this. House and Wilson, Rodney and Sheppard (sort of...), Q and Picard, Snape and Harry *g*