Posting about some fics I've already read that I didn't comment on when others rec'd, and also about some that I've read for the first time due to this thread.
The Tale of the Gallant Familiar. It's a Naruto/ZnT crossover which starts in the predictable fashion for all ZnT crossovers, but with Jiraya as the summons, right after he had his arm cut off and was thrown into the sea. Only one 10k word chapter up so far, but it looks like the quality is pretty decent.
This could use a little bit of revision/proofreading, but yeah, it seems promising.
Puella Stellae Madoka Magica: It's what would happen if the Madoka world was a lost world stuck in a Warp storm, Kyubey was a daemon, and Empie's spirit managed to make his way there in pursuit of a certain unborn goddess. Things escalate from there. One of the best crossovers for both 40K and PMMM I've ever read. God-tier.
I'm personally hesitant to call this fic god-tier. When I think god-tier, I think of Prince of the Dark Kingdom, Dauntless and The Green Sun Illuminates the Void. He Who Fights Monsters and NGE: Genocide;Extended (I really need to re-read that) fall somewhere around there. This is definitely a good fic, though. I was put off early-on because I didn't realize at the time that the author uses distinct writing styles for either setting, and I wasn't a fan of the super minimalism for the PMMM scenes. Once I got to the point where everything meshes together, though, I came to appreciate it.
Cast in Gold: NGE/Exalted crossover.
Cast in Gold is kind of complicated.
Shinji gets the exaltation, and it kind of makes sense, but it throws the dynamics (inter-personal, inter-entity regarding the various organizations and governments) all over the place. I do like Cast in Gold, but I'm not sure where it's headed anymore considering the last handful of chapters.
He Who Fights Monsters: An absolutely brutal For Want of a Nail fic in the Rosario + Vampire world. Read if you want a story about an ordinary human struggling to survive in a place full of literal monsters that would literally eat him if they knew he was human, full of intense fights that run on pure luck and adrenaline, meaningful character development, quite a bit of tongue-in-cheek humor, and an absolutely brilliant ending. I can't recommend this enough. In fact, I think I'm about due for another reread...
Yes. All of this. Even if you have no idea what Rosario + Vampire is, find out the basic premise and read this fic. If you're familiar you'll be able to appreciate everything that happens more, but it's not really necessary. Also, it's NSFW for multiple reasons, but it's an incredibly good fic. Hawker is also a great author, but his work is strewn all over the internet, especially on non-mainstream fandom-only sites.
The Hill of Swords. Fate/stay night. It is the freaking Hill of Swords. It is excellent. It should be read. You should read it. I don't care who "you" is directed to. Read.
Bumping this. This is the only fic I've read more than like 3 times (I sometimes re-read NGE fics that I read ages ago), and I think I've read it a total of 5 or 6 times.
It's just... so good. Gabriel Blessing really needs to go back and proofread everything. It's pretty unpolished in that sense. It should also be noted that it is kind of a love or hate fic, but I just absolutely love it. Gabriel Blessing's other work is pretty damn good, but THoS is something special.
Oh, also? This fic is the reason why I read all of the Familiar of Zero manga as well as read all of Fate/stay Night. This fic was recommended to me by a friend, promising excellence if only I were knowledgeable of the setting, and I wasn't disappointed. Since then I've read three other series in order to read GB's other fanfics. I've only ever done that for one other author.
I don't think No Gods, Only Guns has been mentioned yet. Excellent read so far. Mass Effect/Borderlands that is somewhat unique in that it's not merely "character X from universa A goes to universe B", instead merging the two.
Read all that there is of this so far. It's pretty darned good. I get a definite Glorious Shotgun Princess vibe from it, but it's much more fitting in this considering it's a crossover that involves Borderlands. The meshing of the worlds isn't fully fleshed out yet, but the cross-integration of the characters from both settings is really well-done. This fic has a ridiculously large main cast, which is fitting for both settings.
Edit: BAH! Forgot to mention
Kyon: Big Damn Hero. From the site:
Kyon -- Big Damn Hero
A Tvtropes website/Haruhi crossover. Kyon with a beam saber. Haruhi aware of her powers. An unsubtle harem plot. Did I mention the Higurashi crossover? Now say it with a straight face - I dare you.
The first arc? "In Media Res Prologue"
The first chapter? "Exactly What It Says On The Tin"
It's not really crack, though. There's some very serious plot that goes on, but the self-aware nature and lampshading of tropes makes it even more enjoyable. You'll be able to really appreciate this with only a basic understanding of the Haruhi setting, although I think there's a tad bit of spoilers if you haven't watched the anime.
Double Edit:
Oh, and my entry for the mega-ridiculous-crossover fic?
Unequally Rational and EmotionalIt started out pretty interesting with a very real premise in the Mahou Sensei Negima setting. Somewhere along the way, author took some crack that had shot up some crack that had been condensed and concentrated in a vat of crack and then vomited all over the story. I can't even begin to care how many anime/manga/etc. series this has crossed over, but it should be noted that at least DC comics is also in there, probably Marvel too. Also, it has crossed over
with other mega-ridiculous-crossover fanfiction, some of them with the consent of the author and then the other fics have chapters that include stuff that happens in UR&E. I had to stop reading this because nothing in my life made sense anymore.