Looking for decent fanfic for these:
Mass Effect
Glorious Shotgun Princess by Gregg Landsmann. It's a crossover with Exalted.
Also, for Mass Effect x Warhammer40k, try
Hammerhand and its sequel
Angels of the Storm.
Dragon Age (preferably Origins)
Everything by
beanball. Start with The Orbs of Arastani.
Naruto
I'll have to go digging, but one I'm currently reading and really liking is
Naruto: Genkyouien. Beware, it has absolutely wonderful crack in it.
Oh, there's also
Naruto: Game of the Year Edition, which is also silly.
And S'TarKan's
Team 8, which is not silly. It's pretty darn good.
Harry Potter
Easy-peasy. You ready?
Harry Potter and the Methods of Rationality Oh I see you've already read it.
Harry Potter and the Nightmares of Futures PastPrince of the Dark KingdomI would recommend those for standard reading. Doesn't even matter if you know HP or not, those three fics are amazing.
Warhammer 40k
The only one I can think of right now is
The God of Death, which is a Warcraft/Warhammer40k crossover. You can also check out
The Guy Who Cried Grendel, which is a recount of a Dark Heresy campaign that has been canonized (at least to some degree) by Games Workshop.
Also good was Shinji and WH40K which is basically Evangelion if the main character were raised by Orks.
I was hesitant to suggest that and/or Thousand Shinji, because they are far more of Evangelion fics with WH40k flavor. Also, it's more like if the main character were raised by a representative of each of the main races of WH40k. There is certainly Ork influence though.
I've always been more of a Harry Potter fan though. I'll be the first to admit that I have weird taste, though. I can recommend:
Harry Potter and the Natural 20 Premise: a boy wizard from the D&D universe gets sent to Hogwarts. Comedy.
Damn, I forgot to list this one as well. I second this rec.