When I gave my Mary Sue talk, it was at a quasi-academic conference in a session on fans and gender. One of my co-panelists was Olivia Mendoza, a student at Ithaca College; she gave a great presentation on genderswapping fanfic, focusing on the Rule 63 variant in Avengers fandom.
She's kindly put her slides up on Dropbox; take a look! And feel free to leave recommendations for your favorite fics on the topic as well as any comments. (I'll be dropping her a link to this post.)
I already recommended one of my favorites here, which swaps both the Sherlock versions of Holmes and Watson:
Boston Marriage (75193 words) by pendrecarc
Fandom: Sherlock (BBC) - Fandom
Warnings: Author Chose Not To Use Archive Warnings
Relationships: Sherlock Holmes/expensive violins, John Watson/OC
Characters: Ensemble Cast - Character
Additional Tags: Genderswap, Case Fic, Big Bang Challenge, Women Being Awesome, Bechdel Test Pass
Series: Part 1 of Suite for Strings and Steel
Summary: (see notes for warnings)
In which Jo Watson tries to take this therapy business into her own hands, London produces enough crimes of interest to satisfy even Sherlock Holmes, and the Bechdel test doesn't know what hit it. Game on.