As far as I can see, and I am over-dosing on Alias fic at the moment, it is over-whelmingly het - syd/vaughn or syd/sark. Slash is rare and vaughn/sark even harder to find, which as you say is slightly amazing given the amount of times those two lovely boys spend together, fighting and even hot, and naked. I swear the end of season three is an ode to HoYay. Seriously. There is complete gratuitous nakedness between boys (while being totured) and snarky one-liners about masculinity. And lets just face it - in the finale, despite being a sociopath, but oh so cute, Vaughn ( who really cannot be that gormless as he has been living a lie and covering that up ) lets Sark go!!!!! In the epilogue, 7 years later, he has this cute but shifty look when Syd teases him about this. I have this whole thing where they meet up once a year, fight, have sex and then go back to wifey/arms dealing. It is love I tell you.