Ok, here's my super large list of fanfic recommendations!:
*The Missing Piece: The most awesomest story EVER!!! And my first Ouran fanfic. KyoHaru. Rated T
Summary: Kyoya and Haruhi have been dating in secret since the beach house. Now after the Ouran Fair the two face a new problem as keeping their secret relationship hidden becomes a lot harder, but do they even want to keep it secret from everyone anymore?
27 long chapters and finally complete!LINK:
http://www.fanfiction.net/s/7503052/1/The_bMissing_b_bPiece_b *A Shadow Queen Chosen: KyoHaru. Rated M
Summary: This takes over from the anime episode 8, when Kyoya attempts to teach Haruhi a lesson.
9 chapters and still ongoing.LINK:
http://www.fanfiction.net/s/3459271/1/A_bShadow_b_bQueen_b_bChosen_b *An Exchange of Few Words: KyoHaru. Rated K+
Summary: As the one girl in a club full of men, it was bound to happen. Haruhi just didn't expect it to happen with him. And she really didn't expect to enjoy it.
7 chapters and still ongoing.LINK:
http://www.fanfiction.net/s/3129931/1/An_bExchange_b_of_bFew_b_bWords_b *Blackberries and Butterflies: KyoHaru. Rated M
Summary: The dreaded AB bloodtype is harassed yet again, but does Haruhi only see him as the host club's demon lord? Kaoru begins to notice a difference in Kyouya's behavior and attempts to nudge him along towards Haruhi.
A long oneshot and complete!LINK:
http://www.fanfiction.net/s/5879459/1/bBlackberries_b_and_bButterflies_b *Crystal Clear: KyoHaru. Rated T
Summary: "What does Tamaki have that I lack?" Kyouya asked quietly. He didn't expect Haruhi to answer. Actually, he really didn't even mean to say that out loud. It just sort of escaped his lips before he could really think, something he tried to avoid doing.
18 chapters and complete!LINK:
http://www.fanfiction.net/s/5504663/1/bCrystal_b_bClear_b *Deep Waters: KyoHaru. Rated T
Summary: A rainstorm floods Haruhi's apartment, making it unlivable. When Kyoya & Tamaki find out, they both try to help, much to Haruhi's chagrin. And will their kindness make Haruhi realize her feelings for a certain someone? Haruhi/Kyoya & Slight Haruhi/Tamaki.
28 chapters and complete!LINK:
http://www.fanfiction.net/s/7022759/1/bDeep_b_bWaters_b *How To Kill Boredom: KyoHaru. Rated M
Summary: Haruhi was bored and as a result she sent a rather tempting message to Kyoya accidentally. How would Kyoya react? Read and find out! This is my first LEMON! You have been warned!
A long oneshot and complete!LINK:
http://www.fanfiction.net/s/4617550/1/bHow_b_to_bKill_b_bBoredom_b *Love and Marriage: KyoHaru. Rated M
Summary: This is a sequel to 'How to Kill Boredom'. Because of that 'little' encounter, Haruhi got pregnant which resulted in a 'Shotgun Wedding'. Now let's look into the life of the newly weds. KyoyaXHaruhi. Warning: Lemony content. Kids stay away!
15 chapters and complete!LINK:
http://www.fanfiction.net/s/4617568/1/bLove_b_and_bMarriage_b *It's Only A Kiss: KyoHaru. Rated T
Summary: Just a little fluffy fun I wrote about the forbidden couple...lol
Oneshot and complete!LINK:
http://www.fanfiction.net/s/7927499/1/Its_bOnly_b_bA_b_bKiss_b *Lessons In Love: KyoHaru. Rated M
Summary: Haruhi finds out that she needs a tutor so that she can stay at the academy! She doesn't have the money to hire a tutor and her only friends are in the host club. Only one man is smart enough to help her, but will she be willing to pay his price?
23 chapters and still ongoing!LINK:
http://www.fanfiction.net/s/6553338/1/bLessons_b_in_bLove_b *Letters Written in Ink: KyoHaru. Rated M (The one by lilalexis131, since there are 2 stories with the same title and summary)
Summary: "Haruhi..is something the matter? You seem troubled" Kyouya said softly leaning against the wall. The said girl looked over at him and mumbled out a soft "I have cancer Kyouya-senpai."
19 chapters and complete!LINK:
http://www.fanfiction.net/s/6938460/1/bLetters_b_bWritten_b_In_bInk_b *Living With Kyoya: KyoHaru. Rated K
Summary: Living with Kyoya was not as awful as she first thought it would be. Chap9: Haruhi is pregnant and Kyoya is being... well, Kyoya.
9 chapters and complete!LINK:
http://www.fanfiction.net/s/3373644/1/bLiving_b_with_bKyoya_b *Locked Up: KyoHaru. Rated M
Summary: Kyoya and Haruhi are accidentally locked in the host club room for an entire weekend.
8 chapters and still ongoing.LINK:
http://www.fanfiction.net/s/7416580/1/bLocked_b_bUp_b *Long Term Bet: KyoHaru. Rated K
Summary: Because Hani-sempai will always be rooting for Kyouya. A Kyouya and Haruhi fanfiction from Hani-sempai's point of view.
Oneshot and complete!LINK:
http://www.fanfiction.net/s/7984310/1/bLong_b_bTerm_b_bBet_b *Not A Mistake: HaruXSECRET! (You have to guess) Rated M
Summary: Haruhi's daughter asks if she was born by mistake. Looking for a simple answer, she receives a story instead about the mystery of who her father is. *WARNING* The reviews say who the father is, if you want to guess yourself don't read the reviews.
3 chapters and complete!
LINK:
http://www.fanfiction.net/s/7330661/1/Not_ba_b_bMistake_b *While the Rest were out Sick: KyoHaru. Rated T
Summary: Tamaki, the twins, and the seniors are all out sick with the Flu and the only host's left are Haruhi and Kyoya. Can the two survive the other's sick days without killing eachother or falling for eachother? it's better than it sounds really.
6 chapters and complete!LINK:
http://www.fanfiction.net/s/4727652/1/bWhile_b_the_bRest_b_bwere_b_bout_b_bsick_b *The Road to love: KyoHaru. Rated T
Summary: The other Hosts are back from their ilness' and Kyoya and Haruhi have been found out. Now they have to overcome the challenges coming form every where that threaten to tear them appart. sequel to While the Rest Were Out Sick.
14 chapter and still ongoing.LINK:
http://www.fanfiction.net/s/4760843/1/The_bRoad_b_to_bLove_b *Thunder And Shadows: KyoHaru. Rated T
Summary: If timing were just a little different that night at the beach house... 'Despite the fact that I had seen through his rouse, I couldn't help but admit to myself that in the moment he flung me effortlessly down to the bed… I had no intention of resisting.'
20 chepters and complete!LINK:
http://www.fanfiction.net/s/6547963/1/bThunder_b_and_bShadows_b *Tormenting Waters: KyoHaru. Rated M
Summary: Haruhi was always a very special addition to the host club, but just how special is she really? Can her knight in shining armor come to her rescue when she is in need?
11 chapters and still ongoing.LINK:
http://www.fanfiction.net/s/7518092/1/bTormenting_b_bWaters_b *Until You: KyoHaru. Rated T
Summary: When Haruhi gets in an odd mood and then has to spend the evening with Kyouya as her only company she isn't sure if she will ever be able to figure out why she's in the odd mood. And why is Kyouya caring so much about her mood or her for that matter?
20 chapters and still ongoing.LINK:
http://www.fanfiction.net/s/4873716/1/bUntil_b_bYou_b *Revolution- My most favorite Ouran yaoi couple!!! KyoKao. Rated T
Summary: Kaoru's opinions for his sempai change drastically, and Kyoya finds what he's looking for after a storeroom encounter.
26 chapters and still ongoing.LINK:
http://www.fanfiction.net/s/7469215/1/bRevolution_b ***I missed a few fanfics, so I'll post them up later. Obviously I love KyouyaXHaruhi fics the most! Hopefully you like something from this list!!!