The links below should be considered a starting point, rather than a definitive list. Genderfuck is a conversation which crosses fandom lines, as the theme has a long history; SGA is not the first fandom to use it, and many of the ideas articulated in SGA stories build on what has gone before. Likewise, the conversation is not yet over, and is branching out in new directions all the time.
Another thing to be aware of is that I'm privileging the texts I found most interesting, but they are just a sample: the tip of the proverbial iceburg.
Three Things I Wish People Would Bear In Mind When Writing Genderswap by wychwood. This is a good starting point in the discussion of genderfuck texts, as it includes links to various examples combined with commentary. What makes this particularly interesting is that the linked stories range much more widely in quality than most recommendation lists. ETA: Don't forget to look at the comment threads too, as that is where much of the interaction takes place (and that goes for all the other links here as well).
Genderfuck Recs by fairestcat. This lists some of the more sophisticated stories on the genderfuck theme. I don't like all of them, but several are favourites of mine. You'll see that one of them is by me--I wrote it because I was so tired of the "male" protagonist hating his transformed-female body. It was starting to really bug me.
ETA Feb 2008: There have been some new rec posts on this theme. Genderswitch (for 14 Valentines) by incidental_fire; and Slashy het / het slash -- you decide by monanotlisa.
I've just come back and added this category as an afterthought. I don't have much to put here yet in terms of art/songvids, but I've noticed a growing trend in this area too, existing side-by-side with the fic. For instance:
Tracing for the win (genderfucked John) by pentapus.
ETA Feb 2008: A few months ago there was a brief interest in manipping genderswapped characters, to very interesting effect: Dr Meredith McKay by aretria; and Female John by neths_athari.
Gender and sexuality in three SGA stories by cathexys. This is a new essay by one of the foremost acafans. I often find myself disagreeing with minor aspects of her analyses, but her work is always interesting and insightful, and she certainly has her finger on the pulse of fandom. This essay also links to a previous one which discusses the trend of "We're Not Gay, We Just Love Each Other" (which was brought up at Swancon).
What's more important, the brain or the bits? a poll by trobadora.
Where is all the hermaphroditism? by thelastgoodname.
Some other relevant stuff
"The Seven Basic Plots," Feminism and Fandom by emily_shore, an essay on the lack of "active heroines" in literary tropes.
Of the blend of feminine and masculine in slash by paceus.
Fanon characterisation and access character: feminisation or heroinisation? by cimness, a fascinating discussion of the way in which fans privilege the point of view of certain characters.
There She is Again... Like a Turd in the Fandom Pool... by slytherincesss, an essay giving a counter argument that slash does not promote pro-gay values.
Slash Writers' Demographics a poll by skuf, which has some biases (eg. in the definition of "queer") but is still interesting.
ETA: You can find more fiction on this and related themes at the Crossroads Archive, under such categories as Transformations - Gender-bending, Mpreg (male pregnancy), and Kink - Fetishism & crossdressing. If you want more after that, you can find links to stories, authors and archives in my SGA Primer, and at rec_room.
You can find more discussion on various fannish topics at metafandom.