Good FanFiction on fanfiction.net?

I've answered a lot of questions like this before, so I'm going to make this my compiled list of recommendations. These will be approximately in order of how much I like/recommend them. I'm also going to skips some of the most obviously popular stories since you've probably already tried them.

Harry Potter:

A Long Journey Home by Rakeesh - female-Harry, time travel slow updates, long story, Adventure/Friendship/Historical - Female-Harry takes a trip to Egypt with Ron and Hermione. "Harry" ends up being sent into the past by accident. I am really trying to avoid spoiling anything, but it's a really awesome story. You should try at least a couple chapters.

The Lie I've Lived - Harry/Fleur, memory weirdness, complete, long story, Action/Romance - Best Harry/Fleur story I've read. Aside from the original premise, everything in the story is fairly believable. Harry is certainly a better hero than he was in canon, but he also has greater obstacles to overcome.

Delenda Est - Harry/Bellatrix, time-travel, complete, long story with sequel, Adventure/Romance (some) - Best Bellatrix/Harry story I've read. Harry's a bit passive at times, which can be annoying, but the story keeps up its pace.

Harry Potter and the Distaff Side by Clell65619 - dimensional travel, Harry/Luna, hiatus, long story, Action/Romance - Harry gets sent to a world where almost everyone's genders are reversed. It's really interesting seeing what Clell came up with for that world.

Brutal Harry by Lords Fire - Harry/Hermione, complete, long story with sequel, Action/Friendship/Abuse - Being abused as a child (much worse than in canon) really messed Harry up. This story explored how a more powerful, but certainly not well-adjusted, Harry would go through Hogwarts. Villains are made more powerful as well.

RuneMaster - Harry/Fleur and later Harry/Luna, long story Action/Romance - Harry develops a talent for Ancient Runes, and it takes him places. Some of the plot devices used are a little questionable, but it still is among my favorite stories. Harry definitely becomes a badass, but it is something of a natural progression.

Allure Immune Harry by Racke PM - Harry/Fleur, oneshot, Romance - short, sweet, and hilarious. It takes the idea that Harry is immune to Fleur's allure and runs with a potential direction that could have gone.

Protection from Nargles by Arpad Hrunta - Harry/Luna, medium length, complete with sequel, Romance - What if Harry hadn't jumped away from the mistletoe when Luna pointed it out in the DA? I've never seen a better Harry/Luna romance, where Luna keeps her canon character. She's still insightful, flighty, and slightly crazy, but it really works with this story. It's sequel has some more angst though.

On a Pale Horse: dimensional travel, medium length, ongoing, Humor/Horror(ish) - Harry is the Master of Death, which basically makes him the Grim Reaper. After millennia of growing steadily more bored, insane, and inhuman, he is summoned to another universe to take care of their Voldemort problem. I almost didn't read it due to it's super-powered Harry cliche, but I'm really glad I did. There's very little focus on actually fighting against adversaries, and much more focus on how a completely insane Grim Reaper would amuse himself in book five or six (I can't remember exactly when), and what canon-ish Harry's relationship with his counterpart would be like.

Growing and Standing by Crazy Mishka - Harry/Hermione, complete, short story, Romance/Friendship/Disability - Hermione is deaf. Harry tries to become her friend in fourth year. It's another very heartwarming story, and I haven't seen any other disability story focus so much on the relationships between people and how the disability affects them.

Catechism: medium length, hiatus, Friendship/Abuse - What if the Dursleys were much, much worse, but also much, much smarter about it? What if Harry was convinced that magic was evil, that he was worthless, and that the Dursleys represented all that is right and good in this world? This story will make you sad and make you sick, but it's a really well written, scary, and interesting depiction of what Harry could have been like.

The Arithmancer by White Squirrel - Hermione-centric, semi-canon-following, on-going, long story, Adventure/Friendhsip, later pairings - The story is sprinkled with alternative takes on canon and a lot of interesting ideas.

Harry Potter and the World Beneath - Harry/Fleur, wild-Harry, slow updates, medium length, Adventure - Harry runs away from the Dursleys and literally falls into another world where he eventually becomes something of a Tarzan (mostly losing his humanity).

Deprived - Harry/Fleur, mercenary-Harry, hiatus, long story, Action/Romance (some) - If you can get past the premise that Harry became a complete badass before the age of 14, and the Potter-bashing, it's a really interesting story. It really gets into the mindset of someone who's not completely sane.

The Lords of War and Thunder - Harry/Fleur, slow updates, medium length, Romance/Family - Harry is three years older, and has a brother who is the Boy-Who-Lived (parents still dead). Harry tries to protect his brother when he is entered into the Triwizard Tournament. It's very relationship-centric, and has a cute, if very quick, build-up to the two pairings.

Seventh Horcrux by Emerald Ashes - Complete, long story, Humor - Voldemort's horcrux takes over Harry pretty much immediately after 1981. But Voldemort is completely and totally insane, and only ever really wanted the Defense professor position anyway. It's completely hilarious.

Thoughts of Pudding 2012 by Brian64 - Harry/Luna/Hermione, hiatus, medium length, Romance - One of the only believably written multi-partner stories I've found that includes showing how the threesome got together.

Naruto:

A Drop of Poison by Angel of Snapdragons - Ongoing, long story, Adventure - Nice Hokage and mentor(ish) Iruka, really awesome skills that don't involve a hack like a bloodline, but do require significant time to develop. No pairings so far.

A Teacher's Glory by Larry Huss - Complete, long story, Action/Friendship - Same Team 7, different instructor, emphasis on teamwork and the professional side of being a ninja. Canon pairings eventually.

Cleaning no Jutsu by Erisah Mae - OC/Guy, medium length, complete, Romance - OC-centric, but no Mary Sue. Very funny and cute.

Freedom in the Eyes of Another by Oroburos69 (on AO3) - Complete, short story, Torture/Psychological - Sakura-centric, torture and recover themes, more realistic ninja world, interesting psychological perspective.

Konoha Maelstrom by Formulaic - Hiatus, medium length, Adventure - Naruto-centric, building up better skills based on canon abilities, jutsu theory, sealing.

I Am NOT Going Through Puberty Again - Naruto/Hinata, Sasuke/Sakura, Ongoing, long story, Humor/Crack - Hilarious story where the 4 characters get accidentally sent back in time (from the end of the canon timeline) and most just screw around.

Naruto: Chosen Vessel by BlueGlass54 - Hiatus, long story, Adventure/Friendship - Different team (Naruto, Ino, Kiba, Asuma), different Kyuubi (but in no way benevolent), interesting missions and character dynamics.

Naruto: Myoushuu no Fuuin by May Wren - Focusing on learning different kinds of sealing techniques and their applications, interesting

Steal My Thunder God - Time travel, hiatus, medium length, Adventure/Political - An older Naruto accidentally goes back in time when learning the Hirashin, and ends up taking the Yondaime's place after his death. Naruto's more powerful, but mostly he's just barely keeping ahead of disaster so far.

Team 7's Ascension: Blood Wings by Eilyfe - Same Team 7, extremely different training methods, more team-centric than Naruto-centric

A political perspective by MueraRashaye (AO3) - Kakashi didn't intend to pass Team 7, but once he did, he was going to train the heck out of them.

Teach Your Children Well by AvacadoLove - Time travel, complete, medium length, Teamwork theme - Kakashi goes back in time and tries to fix everything. I really like the different take on how he'd feel about Sasuke. It's kind of a pre-slash Kakashi/Iruka, but it doesn't really get into that.

Patriot's Dawn by The Pro - Different team (Naruto, Ino, Kiba, Asuma), follows canon a bit, but is fairly interesting

Could you specify if you're looking for slash fanfics or heterosexual? Because I don't know what I should recommend ;D