The Buggy Ring arc. Sanji figuring out what Zoro had planned without a word spoken, then a flawless team combo to take out the giant.
And of course the first person Sanji meets upon returning to Sabaody is Zoro and vice versa. They waste no time getting on each other's nerves.
On Punk Hazard when Sanji switched bodies with Nami. Sanji slips on the snow, Zoro grabs his hand to keep him from falling, upon which Brook comments it looks romantic. Zoro immediatly makes a face, throws Sanji to the ground and states "I don't care what happens to you!". Total tsundere moment.
Though he could very well have been thinking about Nami at that time. Zoro is fairly protective of the girls.
The Kalifa/Nami fight was equal parts fanservice and Les Yay. Is it really necessary to practically 'spoon' with your opponent to use Kalifa's devil fruit power?
Kalifa basically gropes Nami to make her slippery. Please note that Nami is shown to be slippery everywhere visible.
Plus, Kalifa gets this reaction from Nami before their fight in Enies Lobby:
Emperor Ivankov of Kamabakka Island is very loyal to Dragon. So much so that he was willing to wait for Dragon's signal while stuck in Impel Down and is only convinced to leave once he finds out that Luffy is Dragon's son. He then makes protecting Luffy his top priority, even stating that he wouldn't be able to face Dragon if he allowed his son to die in battle.
Regarding that first part, he is living in luxury in his own hollowed-out section of Impel Down surrounded by people who practically worship him, so waiting for Dragon's signal isn't all that impressive a sacrifice.
Probably doesn't help that Ivankov can change his/her gender at will...
It's not hard to picture Chaka and Pell as being partners in more than one sense of the word.
Chaka: I still... can't accept your death. I can't even shed tears. Why is this, Pell?
Brook and Yorki had an awful lot of smiling and touching going on, especially in the anime. Which just makes that flashback even more depressing when you get to all the inevitable tragedy.
Coby and Helmeppo skirt the edge between very good friends and boyfriends. The filler doesn't really help. Taking Coby's fanboyish adoration of Luffy into account, an argument could also be made for a Helmeppo-Coby-Luffy triangle.
Calgara and Norland from the Skypeia Arc flashbacks. The entire arc hinged around their tragic separation and the suffering both of their descendants endured as a result.
The Danish translator apparently ships them, as one of Noland's crew members' lines is translated from "Look at how friendly they are with each other now" to "From the look of it, you would think they were lovers".
Usopp and Luffy are always touching and dancing together, constantly in each other's company and whenever they are apart Usopp tends to talk about his captain an awful lot...
Though usually only seen in filler, whenever you see the crew sleep, Usopp and Luffy are always next to each other, add to that "next to" oftentimes ending up as on top of/entwined.
Also, Luffy being tempted into looking at the bathing Nami was apparently because Usopp is a "bad influence" on him. Sure straight males of late adolescence perve on women together, but Luffy is basically sexless. Usopp is capable of getting Luffy to express sexual interest, nothing more needs to be said. (Though that scene was also prime Luffy/Nami bait).
In a much creepier way, it's possible to see the relationship between Chopper and Zoro like this. They sleep next to each other, Chopper is always clinging to Zoro's body and Zoro washes his back. He's one of the few people Zoro will rescue or aid without complaining or getting grumpy about.
Boa Hancock, a woman whose primary power (and negotiating tactic) is to make everyone fall in love with her. Everyone.
Doflamingo calling Caesar his cute/indispensable subordinate, Caesar responds in joy and tries to run to him while surrounded by hearts!
Sanjida (who's supposedly a female Sanji in the Obahan Time special, though she's still voiced by Sanji's voice actor) likes to touch other females.
Many fans' fantasies of Law and Luffy as a polar opposite couple have only been fueled by Luffy refusing to let Law leave their alliance and then carrying Law along with him.
Prior to this, in the arrangement of the alliance itself many Straw Hats cautioned Luffy against it, citing that many pirates are backstabbing by nature and also Law's dark reputation. Luffy's response to his friends is close-minded insistence that the one who saved his life after Marineford two years ago is definitely a good person. Mind, we still have no idea if Law had deeper reasons for doing this for him, and claimed it was on a whim. But either way Luffy is extremely grateful and is very jolly in Law's company.
No matter how Law protested he and Luffy's alliance was over, Luffy was determined to save him from Doflamingo. The rescue proceeded to have hijinks in which Law may not have been handled as delicately as he probably should have, but even in the end after his cuffs are removed he says that maybe getting carried by Luffy was a good thing, as he was able to conserve his strength. Never mind all the stress he suffered and all his protests to get him un-cuffed, huh?
The Reveal that Law wants revenge against Doflamingo for killing the most important person in his life, Corazon, Doflamingo's own brother, has made some fans wonder if Law's going on a Roaring Rampage of Revenge over a broken heart.
Corazon's name literally means 'Heart' in Spanish. Law's crew is called the Heart Pirates. Think about that for a moment...
Law's obsession over Corazon in general, really. Law, who was always presented as an ambitious man, is perfectly happy to throw away his life and dreams if it means fulfilling Corazon's last wishes. In addition to that, he named his crew after Corazon, wears a jacket with Corazon's name emblazoned on the back, and tattoos Corazon's namesake all over his body. He even outright stated in chapter 725 that the only reason he decided to survive to this very day was to avenge Corazon. To add fuel to the fire, his last thoughts before succumbing to the gun shot wounds inflicted on him by Doflamingo weren't about his plan or the agonizing pain, but instead they were an interrupted apology to Corazon for failing him. And the kicker? According to some translators, in chapter 749, the kanji used in Law's dialogue when he declared Corazon to be his most cherished person was written in a way that could easily interpreted in a... more than platonic fashion. Let that stew in your brains for a moment...
The fact that Law is also one of the only people immune to Boa Hancock's charms has thrown further fuel to the fire. While most originally wrote it off as Not Distracted by the Sexy, the revelations about Corazon now have many thinking it leans Law towards Ambiguously Gay at the very least.