Since I am still reading books about fan writing that highlight specific types of stories, I have started thinking about stories I have read that serve as examples of those tropes. So here are some more recommendations from different fandoms.
Crossover
Relatives and Relativity by Yahtzee (Doctor Who/Sense and Sensibility)
I found "Relatives" referenced in a book about fanfiction and because I recognized the author as the writer of the best "Alias" story I ever read ("Irenicon", which is an epic novel featuring a scene that would turn out to predict a scene in the series finale almost exactly) I had to find it on AO3. It is the sort of fic I would recommend to anybody who disparages fanfiction as crap.
mpreg or Alpha/Beta/Omega:
Unexpected Treasure by Vanessa (Lord of the Rings RPF)
Organic Chemistry by cuddlefish (Sherlock)
One of the changes I've witnessed in my years of participation in fandom is a shift in this trope. From the lengthy Children of Men setup of Vanessa's story (which is also a fantastic example of Real Person AU) to the invention of the A/B/O universe which can be invoked for any story in any universe without any further explanation needed. cuddlefish's story is an excellent example of the potential of Alpha/Omega stories. Sort of like "Handmaid's Tale" in its highlighting of the absurdity of overtly patriarchal society, but not as bleak.
BDSM
Collared by gemjam (Lost)
I was challenged to come up with an example of a good BDSM fic in the wake of "Fifty Shades of Grey" (which is at times dangerously clueless about kink or sex in general). This was the first story to come to mind. I'm sure I could find other examples, but this story felt like the best counterpoint to "Grey" specifically as gemjam takes pains to make sure the characters are SAFE and not co-opting a lifestyle to mask their mental and emotional issues.
Fuck or Die
Take What We're Given by Solitary_Endeavor (Sherlock)
I mentioned in a recap that the Fuck or Die trope is very difficult to pull off well. I was specifically thinking of this story at the time as an example of one that does. Somehow the contrivance required to manipulate such an encounter into being doesn't seem all that forced or out of character.