Sailor Moon codified many of the tropes for the Magical Girl genre, including the trend of subtext that magical girls are lesbians.
The manga was already leaning on Les Yay, given its girl power themes and onetoken boyfriend among an otherwise all-female group that become True Companions; in the Stars arc of the manga Rei and Minako even discuss giving up dating because they'd rather be protecting their Princess. (Of course celibacy does not equal Les Yay, but if they want to give up dating and be with each other, then that's a different story.) There's also the fact that Sailor Uranus and Sailor Neptune are in a lesbian relationship which ends in a Has Two Mommies situation when they adopt the reincarnated Sailor Saturn. (Arguably more of a Has Three Mommies situation since Sailor Pluto does help out.) The anime, naturally, took all of this and ramped it Up to Eleven, especially in the hands of the director who eventually went on to make Revolutionary Girl Utena.
In regards to Ho Yay, the R movie had a male alien named Fiore who was in love with Mamoru mainly because of how kind Mamoru was to him (giving him a rose that Usagi had given him) when they were kids. He expresses jealousy towards Usagi upon finding out that she's Mamoru's girlfriend and even tries to kill her.
There was also one of the victims of the day in the Super S series: Yoshiki Usai, who was heavily implied to be gay and in some sort of relationship with his assistant. Fish-Eye targets him and doesn't bother to pretend to be a woman this time.
Not to mention, the English dub turned Yoshiki Usai and his assistant into brothers and considering that they have previously tried (and failed) to cover up Michiru and Haruka's relationship by making them into cousins...
In the manga Bifauxnen Haruka was bold enough to steal a kiss from Usagi. Actually it was more then one kiss; Usagi figures out that Haruka is Sailor Uranus because they kiss the same way. They also had a few shippy moments in the anime, with one scene where Haruka hugged Usagi close to her when protecting her, so close that Usagi could smell her perfume, Haruka flirted with her in an episode or two, and danced with her at a party while dressed in a tuxedo. Not to mention, there are some parallels to the bits of jealousy that Usagi feels when she sees Michiru talking to Mamoru... to the ones that Mamoru himself feels when he sees Haruka and Usagi hanging out. (Meaning that Mamoru does see a girl like Haruka as a prospect rival for Usagi, until it's all cleared up.)
About the Usagi/Haruka dance, when Michiru asks to dance with Mamoru, Usagi objects...until she's offered a dance with Haruka in exchange, and she instantly agrees to dance with Haruka. There dance was rather romantic too...with tons of sparkles and both looked rather happy.
Also, there was one episode of Makoto thinking that Haruka's so absolutely cool that she winds up crushing on her (despite this being after The Reveal of Haruka's real gender).
In the anime, Haruka flirts with a lot of girls, including Usagi and a hotel maid who appears to reciprocate (or at least be flustered). In the latter case, Michiru walked in the room when Haruka was putting the moves on said maid and seemingly acts jealous. Hilarity Ensues.
Because of her flirtatious nature and Even the Girls Want Her, Haruka has Les Yay with pretty much every girl she runs across who isn't an enemy. The inner senshi are, except in episodes where it's actually a plot point, pretty open about their girl-crushes on Haruka.
Sailor Lead Crow and Sailor Aluminum Siren are villains in the last season, Sailor Stars, who have a very good degree of Les Yay. They act like a Slap-Slap-Kiss couple and eventually, when Aluminum Siren dies Lead Crow is extremely heartbroken.
Not to mention that Sailor Lead Crow spends much of her remaining screen time mourning Sailor Aluminum Siren's death and saying things like "Siren loved amusement parks.". Plus she tearfully apologizes to Siren just before she dies by being sucked into a black hole.
Makoto/Ami seems to be a popular pairing, mainly from the anime. Most of that comes from an episode in Super S where they are at a college dance party and none of the men want to dance with Makoto because she's "too tall" for them. Well, except for Tigers-Eye but he's just using her for his villainous plot. Ami on the other hand, was the only person who genuinely wanted to dance with Makoto and doesn't seem to think that she's too tall.
Also, Rei Hino also invokes this trope at times that Even the Girls Want Her and the idol of her all-girls school. The side-story of Minako attending Rei's school is full of Les Yay involving Rei.
Hell, in the manga Act that introduces Rei, Usagi first meets her on a bus and then decides to follow her around because she's pretty. When Rei mistakes Usagi for an evil spirit and uses one of her "Evil Spirits Begone" talismans on her and apologizes for it, Usagi thinks to herself that she can forgive anyone who's that beautiful.
And of course, Hotaru/Chibi-Usa. The Stars manga includes a scene of them holding hands; when Usagi points this out, Hotaru basically says 'Don't you hold hands with Mamoru?'
This quote from the manga: "It's strange, isn't it? We're both girls, but it must have been fate that we met". When you consider fate and destiny and the role they played in Usagi and Mamoru's relationship, this is a Big Deal.
There's some Foe Yay of sorts between Usagi/Serena and En/Ann in the detention episode of the filler arc. Despite being rivals for Mamoru, Usagi is super nice and friendly to "Natsumi" (En's human identity), and at one point, En (weak and delirious because of a lack of energy) starts randomly thinking about how admirable Usagi is and how she's a Worthy Opponent. Then there's the way she sucks energy from Usagi: asking her to stand in front of her, close her eyes, and wait.
Seiya certainly crushed on Usagi, whether as a Gender Bender or Sweet Polly Oliver. You could also argue Les Yay for the hints of Taiki/Ami and Yaten/Minako because Seiya, Taiki, and Yaten really are women, even if they were given gender-bending abilities in the anime.
There's one scene in the anime where Usagi day dreamed that she was kissing Motoki and comes back to reality.......only to realize that she was just about to kiss Makoto. Meeeep.
Rei's Not a Date with Maya Touno, a one-shot girl. The other Inners were almost completely sure that they were girlfriends.
In the manga Sailor Cosmos kissed Sailor Moon. Sailor Cosmos is, according to Sailor Ceres, "the ultimate future form of Sailor Moon", and certainly bears an uncanny resemblance to Usagi... which can be interpreted as either Usagi's future self, a future reincarnation of Usagi, or a distant descendant of Usagi who inherited her mantle as Sailor Moon.
Makoto and Minako have some subtext in one episode of the R season. They have a fight over boys and stay mad for almost the whole episode. Then Minako says that Makoto's ex-boyfriend didn't know how to appreciate girls and how she wants Makoto to be happy, and they make up.
In an episode of R Chibiusa causes the inside of a restaurant to go into zero-gravity. All the girls are inside and start floating. Rei's head floats right up Minako's skirt. From the English dub:
Raye: What a totally weird feeling.
Mina: Uh, do you MIND!
The picture quote bears some explanation. There were childlike villains in the SuperS movie who once said something to the effect of being a child forever being a good thing. Your translation may vary, but Michiru responded that being an adult was better because "there are lots of fun things only grownups can do!" Haruka blushed as red as a tomato.
The first North American dub tried to tone down the subtext by making Michelle say, "Life is full of wonderful experiences from beginning to end!" However, Amara still blushed, at least on the DVD.