The male mentor betraying the female hero - didn't Joss do exactly that plot in, uh, a later series? (Hard to even say which one without whopping big spoilers...)

I don't recall seeing any fics on that premise - I've seen a few dark Giles fics, including one really good twist on "The Gift" where Giles ends up having to kill Dawn since Buffy's sacrifice turns out to do absolutely nothing*, but none where Giles becomes the real big bad. Huh.

* ETA: Damn if it's not the exact story you mention upthread. Great minds have the same small reference pools. :)