1. Sailor Uranus and Sailor Neptune
For many anime fans, this is the big one. So we might as well get it out of the way first.
The relationship between Sailor Senshi Uranus and Neptune might be best known to non-Japanese viewers of the 90s for how it was covered up -- with varying degrees of success. In English-speaking territories, the two were explained to be cousins. Though for one reason or another this didn't wash away the pair's constant flirting. The final effect, for many viewers at the time, was... Likely different than what the localizers intended.
Thankfully, the notion that homosexuality is somehow a "mature" topic has lightened up a bit. If not by much, then at least enough for better dubs and subs of the series to filter their way into the States. So those young and queer can see the girlfriends in all their youthful, empowering action.
And what a pair they make. Uranus and Neptune typically fall on the more pragmatic end of the Senshi spectrum -- going so far as to enter deep cover, and seemingly betray their friends to achieve their goals. In their day-to-day, however, the pair are treated little differently than any other anime couple. That is with warmth pockmarked by good-natured humor, which is usually the result of Uranus's consistent flirting with other women.
The two do die, but only occasionally.
They're not singled out for being gay, either, as biting the dust and making a miraculous recovery is just par for the course on Sailor Moon.
In fact, Uranus and Neptune get the benefit of more heart-wrenching demises. Particularly the second go around, in which they fade from existence together while clutching hands. And since they make a full recovery from oblivion, the duo gets both the best dramatic exit and a joyful return.
2. Kill la Kill's Ryuko and Mako
Kill la Kill comes with more than its share of problems. Its messaging is wobbly, the finale doesn't stick the landing, and its hero -- Ryuko Matoi -- has trouble standing out among its stellar cast of much more colorful characters. One thing the series did have going for it from beginning to end, however, was pacing.
Plots that might take a dozen or so episodes in more mundane shows are resolved within minutes on Kill la Kill; something the show itself made mention of, in case you didn't notice on your own. Episode-long power-up sequences weren't the only filler to hit the floor, however. The series' end-of-show romance between two women is dropped without the grinning, blushing, cringing setup most anime would train you to expect.
Just before Ryuko's literal launch into the final battle, her best friend-cum-sidekick Mako bleats out her desire to go out with the heroine once she makes it back. Which, of course, Mako knows she will. It's a fitting moment for Mako, whose emotions only rise above "indomitable cheerfulness" in flash floods of shouting and gesturing.
Of the relationships on this list, Kill la Kill's is a far cry from the strongest. The back half of the series makes no bones about overt lesbian imagery, but only goes full-bore when evil is afoot. Whereas Mako and Ryuko's stated after-party intentions carry the nonthreatening "purity" (i.e. not much kissing, or anything so vulgar) that's a dime a dozen in anime. Neither of which is a particularly strong case against the show's uneven understanding of its own, often fleshy tropes.
For better and for worse, though, Ryuko and Mako entering a relationship at all is surprising. While Kill la Kill drops more than a few hints about the eventual outcome, they're less recognizable as such in the language of Japanese animation. Instead of being shy about Ryuko's attractiveness, Mako simply won't shut up about it -- something that's easily dismissed as the showrunners' own reminder to the audience.
Ryuko, meanwhile, isn't flustered or shocked by the invitation, but turns the offer into motivation as quickly as it comes. Kill la Kill may suffer from its own breakneck pace at times, but at others it makes for a refreshing take on a medium often too-filled with tropes.