Misaki asking Hatoko to be her second had all the weight of a marriage proposal. Considering that Hatoko's all of five, but still...
Card Captor Sakura
In Card Captor Sakura, Touya and Yukito become one of the Official Couples by the manga's conclusion, Syaoran openly admits that his infatuation with Yukito is much the same as Sakura's, and Sakura herself states she feels the same way around Kaho as she does around Yukito (yet somehow fails to understand the implications). Tomoyo is sincerely in love with Sakura, but during the second half of the manga bows out gracefully and becomes a Shipper on Deck for Sakura and Syaoran instead. Tomoyo's mother had a similarly unrequited affection for Sakura's mother.
In the same episode, they also explain that most of this is because people with power are drawn to each other, often romantically. The logical conclusion is left as an exercise to the reader.
Clover has Gingetsu and Lan, who are awfully close for parole officer and prisoner. For Les Yay, there's Suu and Oruha. There's also Barus and Kazuhiko's innuendo-laden dialogue; Barus is especially fond of Kazuhiko, likes to call him his "prince" and cuddles with his severed hand at night.
Any CLAMP artwork depicting Ora with another female character, usually either Suu or Tsubasa's Sakura, will undoubtedly give off major Les Yay vibes.
There's also subtext between Sayaka and Chitose and Chiho and Chise. Not to mention Kobato's sadness after hearing about the unnamed woman's divorce... It just seems Kobato will become the next Card Captor Sakura...
The second season of the anime version has Hikaru and Nova, although it's (mostly) one-sided (Nova takes her love for Hikaru to a psychotic degree).
Not to mention Presea's attention to Hikaru early on, and Hikaru's practically drooling over Fuu at first.
Innouva basically being in love with Zagato...
RGVeda features a great deal of Les Yay thanks to Kedappa-ou and Souma, who are canonically in love and devoted to each other.
Taishakuten was tragically in love with Ashura-ou, who agreed to indulge the former's affections for one night only in return for a rather large favour.
Seishirou and Subaru share an iconic, if enormously tragic, relationship first in Tokyo Babylon and later in X1999.
Tsubasa Reservoir Chronicle
Tsubasa Reservoir Chronicle has several couples that are Crossovers from other series, in addition to original characters Fay and Kurogane. Over the course of the series, they grow from Vitriolic Best Buds into caring and devoted comrades who function as the group's parents and, in true CLAMP fashion, can easily be construed as more than just friends.
Multiple parallels may be drawn between Kuro Fai and Syao Saku. Fai himself arguably sets up a notable comparison by dubbing Kurogane and himself "Big Puppy" and "Big Kitty", and Syaoran and Sakura "Little Puppy" and "Little Kitty", making his relationship with Kurogane analogous to that of the teenage lovebirds.
Fai also gives Kurogane the affectionate nickname "Daddy". Soon after Mokona, putting two and two together, comes up with a brilliant idea to nickname Fai "Mommy". (And no, Fai never refers so to himself. Considering how hard he tried not to get close to anyone, it would have been unwise.)
Typically, in artwork, the two have complementary colors - white/blue and black/red, and they both carry the Dragon and Phoenix symbolism. (Fai with his tattoo; Kurogane with his sword).
Fai wears a furisode in chapter 167, just before he and Kurogane reconcile. Not only can such an outfit arguably constitute bridal wear, but, in a historical context, was by the male lovers of samurai before the Meiji period. Who's the only samurai in this party? Yeah.
Chapter 185 takes the innuendo to a new high, with Fay arranging for he and Kurogane to have their own room. Ostensibly he simply wants to check Kurogane for injuries, but we are treated to a lovely shot of him casually ripping off Kurogane's armour, and flirtatiously licking blood from his thumb. Fans may extrapolate from that as they choose.
It should also be noted that Kurogane cuts off an arm so that he can rescue Fai from Celes, and never ever complains about it despite the fact that its ill-fitting mechanic replacement causes him pain.
Their cameo appearance at the end of XxxHolic shows Kurogane and Fai displaying some very familiar and tender body language, including Fai dutifully pouring sake for Kurogane.
X also contains strong implications between Kamui and his dark counterpart, and a lesbian relationship between their late mothers.
In chapter 83, after killing Kotori, Fuuma pins Kamui to a wall (by stabbing him through his arms and legs) and puts his face really close, while murmuring seductively and licking his neck. Oh, and it doesn't help that Kamui is steamily whispering Fuuma's name the entire time.
Other fan-popular pairings with a good deal of subtext include Subaru and Kamui, and Fuuma and Seishirou (mostly for the symmetry, it seems).
There's also quite a bit between Fuuma and Kakyou.
Satsuki and Yuzuriha have their fair share of Les Yay.
Doumeki and Watanuki in XxxHoLic, though it looks to be more one-sided for Doumeki, considering that Watanuki sees him as The Rival. Yuko constantly hints and teases Watanuki that he suits Doumeki much better than Himawari does, and she constantly puts them in situations that resembles her matchmaking them. And whenever Himawari herself sees Watanuki and Doumeki interact (read: bicker), she always comments on how they're both so cute and how close they are. Not to mention how much suffering and hell Doumeki has to go through for Watanuki's sake, constantly suffering bad injuries to protect/rescue him. Considering how much Watanuki disliked him and acted like a Jerkass toward him, none of that would really make sense unless Doumeki... um... really really liked him.
In chapter 159 Doumeki reveals to Kohane why he stays with Watanuki. He tells of one day he saw Watanuki standing in the rain, sadly cradling a dead kitten. He hears Watanuki say, "I'll die like this too. Alone." Doumeki then vowed to himself that he wouldn't let that happen. After telling Kohane this she asks him to take care of Watanuki and not to hesitate when the moment comes that he'll be needed.
And then, later, Watanuki appears to start acting like a very typical Tsundere towards Doumeki - especiallyhere... with very obvious romantic connotations.
Doumeki usually calls Watanuki "you" or "dumbass". When he does start calling Watanuki by his name, he does it without the usual expected honorifics.
During the Valentine's Day chapter, if you technically looked at the exchange of chocolate, after the whole mixup, Watanuki gave the chocolate to Doumeki. It's true that in the story, this doesn't carry implications, however, this is xxxHolic, where everything (including the plot) is subtext and symbolism. If you look at the symbolism of Watanuki giving Doumeki chocolate...
And then there's chapter 185, where the heartbroken Watanuki reveals that, after Yuuko disappeared, he decided to make a pact to wait for Yuuko forever, never aging, and never being able to leave the shop, until the day she returns to him. Doumeki's expression when Watanuki tells him is... priceless, to say the least. It looks to be a mixture of being punched in the stomach, exasperation, and a general feeling of, "oh shit, you did not just do that..." much the way an agonized boyfriend would react if his girlfriend told him she was going to remain celibate for the next 500 years or so.
In recent chapters of Doumeki and Watanuki staying together at Yuuko's shop after she disappears you could hear the collective squeeing of fangirls at the sight of them acting like husband and wife a married couple in a situation that has been the set up to countless Yaoi doujinshi. Sadistic Lady Mangaka indeed, and as of chapter 186 they're just doing it on purpose...
This page. Watanuki acting annoyed that Doumeki seems to be spending all his free time coming to see him, only for Mokona to point out that Doumeki is doing it because he's worried about him and want to make sure Watanuki isn't hurt... in heart, or in body. It appears that even Monoka trying to push Watanuki into realizing Doumeki's feelings for him. And the fact that when Monoka told Watanuki that Doumeki was worried about him, Watanuki actually smiled and looked touched.
Recent chapters have Doumeki and Watanuki alone in a bedroom, with Watanuki sprawled out on the floor wearing a loose kimono, discussing about the mating habits of cats, and what it needs for the ideal mate and love. Doumeki seems especially keen on the subject, giving Watanuki meaningful glances while talking about "intercourse"◊ and the one it "longs for." Oh, and did we mention that Watanuki has frequently been portrayed as being cat-like, constantly having illustrations of him with cat ears and tail, with slitty pupils? They were also drinking wine and such.... and Doumeki even filled Watanuki's wine glass for him without receiving any glares or nasty remarks in return...
Chapter l97. Watanuki says Doumeki doesn't really need to stay at the shop since he was only supposed to be running an errand for Watanuki. Doumeki glances away and says he'll leave when he wants to. In response Watanuki almost playfully blows smoke at him. On the next page we get two panels of just Doumeki and Watanuki staring intensely at each other. Though the tension is broken on the next page, it looks like Watanuki was hoping for a different response...
At the beginning of Chapter 204, Watanuki presents to Doumeki a ring specifically for his birthday present. It's a purification tool meant to be worn on the INDEX finger, but Doumeki puts it on the on the wrong finger: The ring finger!
There's subtext not only between Doumeki and Watanuki, but also between Watanuki and Haruka, who he is much more willing to admit fondness for.
Oh, and you know the Zashiki-Warashi, that cute girl that's completely shy and has a huge crush on Watanuki? In all likelihood, "she" is a "he," according to a CLAMP interview where they say that her being female is not necessarily the case. Coupled with the fact that Zashiki-Warashi spirits are normally described as being young boys and rarely being girls, along with how Ame-Warashi usually says "this child" when referring to Zashiki-Warashi instead of actually using a gender.
"Not female" doesn't necessarily mean male... Hana from Gate 7 is genderless as well.
Hana's gender is not stated yet... Series only begun recently, it can still be revealed.
If the Horitsuba Drama CDs count, the fourth CD featured a part where Doumeki put his hands up Watanuki's shirt, and afterwards explains that his hands moved subconsciously on their own. Also at the time he was reading the Zashiki-Warashi's lines from the manga. It Makes Sense in Context.
At the end of chapter 208, when Watanuki talks about chrysanthemum sake cleansing evil and keeping one in good health, Doumeki insists that Watanuki drink some chrysanthemums sake as well and Watanuki agrees with a smile.
Judging by the hints given in Rou ten years or so have gone by, Himawari is married and only visits the store once a year, while Doumeki and Watanuki spend almost every afternoon together. Doumeki goes out to work, brings the groceries, Watanuki cooks and serves the food, then they talk about anything while Watanuki bends around the floor with his clothes almost falling off. Their relationship seems to have almost completely become that of a married couple.
The latest chapters have become increasingly homoerotic, mainly the latest one, in which after granting a ghost woman the wish of being reunited with her long lost lover, Watanuki recieved an umbrella as payement and; while explaining to Doumeki that finding a beautiful woman under an umbrella is an amazing discovery for any man, he walks femininely under said object and winks at his friend.
Of course, when the series ended it is revealed that Doumeki and Watanuki NEVER HAPPENED. In fact, as revealed in the last OAD, Doumeki revealed that he married Kohane. Then in the last chapter, Doumeki died one hundred years later, and Doumeki's grandson ends up watching after Watanuki. To top it all off, we find that Watanuki can leave the shop after living there for one hundred years and that he still decides to wait there for the sake of Yuuko. Ho Yay still? I think not
Not even that stops the Ho Yay. He married Kohane despite the fact that she loves Watanuki more and apparently Word Of God has said that Doumeki loves Watanuki more as well. Which has lead some fans to the conclusion that they married and had kids so that there would be someone to take care of Watanuki in their place since they'll eventually grow old and die.
CLAMP's definition of love has always been...tricky. True love, destined one, most important person, and marriage aren't necessarily aligned. The last OAD seems to reaffirm that Watanuki and Doumeki are bonded by destiny, and it's up to Watanuki to choose if he wants to remain in Doumeki's life. Watanuki says yes. Also note that the entire OAD focuses on Doumeki and Watanuki's relationship. Doumeki is having nightmares which are troubling him just before his marriage. Is it a coincidence that most of Doumeki's dreams contain his first meetings with Watanuki, and the more traumatic incidences involving Watanuki? It's easy to interpret Watanuki as the reason Doumeki finds it difficult to move on to marriage, and hence the nightmares.
And then there's all those times Doumeki saves Watanuki and those Take My Hand moments.
Yűko (of xxxHolic) simply cannot keep her hands off her female clients or her assistant's female friends. She's partial to tilting their faces up while she leans down, making for an 'almost-kissing' pose at least once with each woman Yűko sympathizes with.
Clamp School Detectives has Nokoru and Suoh. Suoh was paired up with a girl half his age, but the manga paid ignorably little attention to this compared to the flashback episode showing how he came to select Nokoru as the "one special person" he would devote the rest of his life to protect.
Gate 7 has Sakura and Tachibana, who might become their newest pairing. They've already been stated to be Yin and Yang in the first chapter. And Sakura has offered to lick Tachibana's wounds...