I personally thought Time Braid was pretty good. The basic premise is "What if the protagonists from Naruto were trapped in the time loop from Groundhog day?" Definitely seconding that one.
Gotta lend my support for this one as well. There's a bare handful of high-quality Naruto fics out there, and this is one of the very best of them. Takes a much more interesting look at the timeloop fic from the perspective of one of the least-used protagonist POVs in the series. It handles a lot of the underlying issues of that sort of time-looping head-on, too, when the people involved all have mental issues of one sort or another.
I'll try not to repeat, but here goes:
NGE: Nobody Dies: 600k words of some of the most entertaining crack you will ever consume. The author is one responsible for Glorious Shotgun Princess and has also put out a lot of smaller NGE fics.
Anything and everything written by
Kenichi618. He's an astonishingly prolific high-quality Naruto fic writer with (I shit you not)
more than five million words across eleven stories, and he typically updates at least once or twice a month. On top of all that, he's a MMA fighter in meatspace, so his fight scenes are technically detailed and perhaps the most realistic I've ever seen in fan-works (and in many published ones).
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.
Uchibi Sasuke: Pure crack. Academy student-aged Sasuke and Naruto end up as friends taking care of all of the Uchiha children after the massacre (the nail being that Itachi asked permission to spare the children of his clan). Not at all serious, but it's bloody hilarious at times.
Thinking in Little Green Boxes: Harry Potter as raised by Deadpool. Nothing more needs to be said.
CoTIW: Unfortunate Meetings: A mishap with the Warp sends a pair of ships, one belonging to da Orkz, the other full of Kriegsmen, into the Magical Girl Lyrical Nanoha 'verse. They crash onto Midchilda and promptly start killing da humies/the heretics. Very well written, but doesn't update very often. Knowledge of both sides helps, but it isn't terribly necessary (beyond knowing that in the MGLN-verse killing magic and non-magical weapons are rare and heavily restricted).
The Empty Cage. Narutoverse, only... the sealing of the Kyuubi went wrong because this verse's Death God's seal is slightly different, and the end result is a dead Fourth and the Kyuubi possessing the corpse of his son. It follows him up through his "childhood" as the fox does its best to mimic humanity. The depiction of the nine-tails is pretty good, walking the line between "always chaotic evil" and that "aww (s)he was just misunderstood" tripe that so many people shovel. Pretty damned good all in all.
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.
The Marker: Short, hasn't updated for a while. Liara T'soni signs up as part of a research crew investigating a certain ship by the name of
USG Ishimura...
The Log: The Log is good. The Log protects. The Log is what crackfic aspires to be.
People Lie: Perhaps the best AU Naruto fic there is. Required reading. Traces of Lovecraftian influence, though it's probably wrong to keep calling them "traces" after the
shoggoth showed up.
Ask Me No Questions: The author's spin-off of the above, switching several of his characters with their canon counterparts.
Cast in Gold: NGE/Exalted crossover.
The Denarian Renegade: First of four stories, a mixing of HP and the Dresden Files worlds, focusing on Harry. A bit too heavy on the power-fantasy for my taste, but you might like it.
A Black Comedy: Basic summary: Harry beats Voldie. Two years later, goes through the veil and ends up in an alternate world, meets up with the Sirius from his world who apparently ended up in the same place. Humor ensues.
The Melody of the Fox: A departure from the rest of the list. It's pretty well written, and the romantic pairing is quite unusual. Worth a look, even if you don't normally go for romances.
The Best Revenge: Oh, this is a really good one. Snape visits the Dursleys early in Harry's life and ends up removing him, essentially treating him as an adopted son. So it's like goodness knows how many other stories in the premise, but this time with a competent writer at the helm. Has a sequel.
XCOM: Second Contact: It's XCOM: EU humanity in the Mass Effect universe. Pretty good story, and since it's only EU (rather than original X-Com) it isn't a complete curbstomp.
Herwald von Einzbern and the Philosopher's Stone: Harry Potter raised by a very special German house of mages, blended HP and Fate/Stay Night worlds. The author is nearing the end of the Chamber of Secrets on his re-write, and there are (le gasp) actual changes rather than a parade through the Stations of the Canon.
Bungle in the Jungle: A Harry Potter fic that comes rather out of left-field. Written entirely in second person (and done so in a way that's both mechanically competent and interesting to read, to boot!). Harry's powerful, but the author has scaled up everything else to match. Adventures in South America with only a handful of canon characters, a complete break from England both in- and out-of-story. Has a sequel.
Basemates: A touching, humorous little ~12k word two-chapter bit piece. Hinata and Neji end up accidentally locking themselves in a basement during a stormy night. Touching in the "emotionally invested" sense, not in the creepy "it's-okay-'cause-we're-cousins-incest" way, by the by.
It's For a Good Cause I Swear: Team 7 timetravel with with a unique angle, and fairly well-written as well.
Naruto: Demon's Path: Starts at age 6. Honestly, the writing starts off pretty bad, and takes a decent length of time to improve. On the bright side, even at the start you can tolerate it well enough to pick up the plot (mostly because it's just juvenile and simplistic rather than full of errors). That, and it has 700,000 words to get better in, and it's good enough to recommend by around halfway through.
First Contact: An Asari exploration ship opens the Sol system in the near-future 21st century. Pretty well written, but slow to update. No crossover.
Magecraft and Wizardry: Unlke literally every other HP/MGLN crossover, this one isn't "Nanoha and Fate attend Hogwarts". Rather, they essentially stole Harry away from the Dursleys when he was being abused in public (IIRC), and it's more about the family dynamic and later the politicking between the English wizards and the Bureau.
I'm also going to toss up a handful of superb fics that don't fall under your requests:
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...
A Green Sun Illuminates the Void: Yet another Zero no Tsukaima fic replacing the summoned Japanese brat with something else. Only this time it's a really damned good author, and the summoning ends up with Louise Exalting. Takes very little time to leave canon territory for new and monstrous places. The author has put out a lot more good work, including some spinoff stories of NGE: Nobody Dies.
Dauntless: A fantastic Code Geass For Want of a Nail fic that also quickly leaves canon territory and never looks back. 96 chapters and 660k words of politics, plotting, battles, family politics, more plotting. Notable in that it has an OC in a central cast postion (out of necessity) who fits the setting and feel of both the story and CG canon absolutely perfectly. The author, well, she's probably one of the best writers I've ever had the fortune to find, not just in fanfiction but in published work as well.
Well. There's my dump for the night. Enjoy!