And then in chapters 589 and 590 both Sasuke and Itachi admit that they love each other and will always love each other.
Whenever Sasuke and Naruto meet post-Timeskip, Naruto tends to act like a battered girlfriend who's convinced that her abusive ex-boyfriend will surely turn into a nice guy again if she only loves him hard enough.
And then there's their reunion in Part II where Sasuke half hugs Naruto, whispers into his ear, and attempts to plunge his sword through his back. And then we see him inside Naruto's mind. That's right, in a manner of speaking, Sasuke has been inside Naruto.
Shippuuden ending 21 features Naruto and Sasuke fighting and getting really close to each other's faces. Although, really, any opening or ending with the two on the screen together has this.
Sasuke and Naruto have a tendency to invade the others personal space and straddle the other when fighting.
And then during the Valley Of The End fight at one point Sasuke finds Naruto and gets real close while grabbing him and pressing his body close to his before kicking him away.
Many people have noticed that Naruto seems to have an obsession with Sasuke following him leaving Konoha.
Borders on romance from Neji's perspective, that is. Hinata only has eyes for Naruto.
Within Akatsuki there is Itachi/Deidara and Pain/Naruto, especially following their fight where Pain crouches in front of a pinned down Naruto and asks him if he managed to "tame" him. Naruto also thinks "Pain's chakra...is inside me..." Deidara/All Uchihas Ever would also qualify, given his hatred of the Sharingan.
Kabuto/Naruto. "After I've become able to completely control Orochimaru-sama's power, I'll return to fight you, Naruto-kun." He has also called Naruto 'cute', is generally polite to him, and appears to possess a peculiar fixation on him.
Also Kabuto/Sasuke. In chapter 581 Kabuto offers a We Can Rule Together speech to Sasuke telling him "No one can understand you as perfectly as I can. I'll be your older brother and stay at your side. Come with me!"
Shikamaru/Tayuya. During his battle with her, Shikamaru attempts to restrain her with his new Shadow technique. Thanks to her expression and the fact the shadows take on the appearance of a hand, it looks like he's molesting her. Then there's the fact that Tayuya immediately returned the favor by casting an illusion which showed Shikamaru in chains and made him think that his arm was melting which caused him to scream in horror while she watched in amusement.
Also worthy of note: said battle ends with Temari (see above) showing up and curb stomping Tayuya. It's very easy to interpret this as Temari bitch-slapping Tayuya for trying to steal her man.
Killerbee/Kisame. Which includes Killerbee getting really close to Kisame and saying he has "pretty eyes" and Kisame mentioning that his sword Samehada really likes Killerbee's chakras, finding them to be "very tasty". In fact, Kisame's sword likes Killerbee's chakra so much that it becomes noticeably bigger, and gains a mouth at the tip that looks suspiciously like Vagina Dentata. He also says that Samehada (his sword) doesn't usually get this excited and that killing Killerbee should be fun. Towards the end of the fight, Kisame strips off his shirt and he and Killerbee get covered inwater and Killerbee's ink. And although Kisame's intention is was to chop off Killerbee's legs so he can't escape this troper had other thoughts upon seeing Killerbee in a vulnerable state on the ground with a shirtless Kisame standing behind him.
Gaara was a bit too obsessed with Sasuke before their fight at the Chuunin exam, basically stalking him while he was training, and calling him his "prey".
There's also the anime-only Ibiki/Pain. "And I will get to know you through pain," Ibiki says as he walks towards Pain's attractive female body, which is in chains. Umm...
Then there's Naruto and the Filler Villain Fuka. She tries to kiss him like four times because her kiss is a Kiss of Death. Even so she still makes some suggestive comments to him like "I'll be taking your body", "those lips of yours will be mine, this time I'll make sure of it", and "lets have some fun together", "lets have a hot kiss", and "I might even spare you if you let me have that body of yours". Not to mention her penchant for invading his personal space or calling him cutie and sweetie while acting all flirtatious the entire time.
The current Mizukage towards Sasuke. She absolutely cannot stop talking about how "good-looking" Sasuke is. Also, "I'll give you a good bye kiss to remember me by". And later sealed off the only exits in the room they were in, leaving only the two of them alone together, so no one would interfere in their fight.
Hidan and Shikamaru. Just watch Hidan's reactions when he got Shikamaru alone in the woods. It almost felt like an Attempted Rape was about to go down. And Hidan looked to be almost orgasming after stabbing Shikamaru.
Madara/Hashirama: It doesn't help that whenever Madara talks about Hashirama, he will always use the term akogare to define how he feels about him (akogare, while usually denoting deep respect, has already become a staple of the Girls Love genre), despite always following up how much he HATES him. Him ranting about how everybody is weak and useless and how Hashirama was the greatest ninja ever!! is not helping at all.
In a recent chapter, a flashback shows him despising Hashirama for killing his little brother Izuna.... even though everyone saw Hashi's brother Tobirama do that. You'd think Madara would remember that sort of detail.
In the last chapter, reinforcements will soon be on the main battlefield, including Sasuke, his Team Taka, Orochimaru, and some more reanimated shinobi.... including Hashirama. The look on Madara's face when he sensed Hashirama's chakra speaks for itself.
Oh it gets better. Madara totally disses Hashirama's wood clone and says he'll wait for the real Hashirama to fight him.
Orochimaru also provoked Naruto once by referring to Sasuke as "my Sasuke".
Also some Naruto/Orochimaru. In episode 29 of the original anime when Naruto was fighting the short-lived battle against Orochimaru who was on top of a giant snake in the Forest of Death, Orochimaru glances down at Naruto, leers at him and says "How very cute. What a cute prey" before wrapping him up in his ridiculously phallic looking tongue, pulling up Naruto's shirt and examining the seal on his stomach before slamming his hand onto it in order to block Naruto's chakra. And in their fight in Shippuden Orochimaru looks really interested upon seeing Naruto go into the Kyuubi state. Upon seeing how much damage Kyuubi! Naruto can cause Orochimaru is shown smiling hugely and saying "This child...intrigues me to no end!"
Naruto/Itachi: Itachi seems genuinely interested in Naruto and his power and has even smiled around him. He also trusts him completely to take care of Sasuke in his place for him, something he doesn't trust anyone else with. A lot his interactions with Naruto carry some Memetic Molester vibes as well.
Kakashi and his frequently (and loudly) self-proclaimed biggest rival Guy Sensei. That smile... and the Berserk Button that results when Kakashi simply ignores him.
Ino/Sakura have a mild rivalry of this nature before they went back to being friends.
Omoi/Ringo: From Ringo telling Omoi that he's her type a to Omoi saying he planned to lick her from the beginning.
Is no one going to mention Kakashi/Obito? Sure, Obito claims to hate him, but both have actually had ample opportunity to kill the other during their fight, opportunities they both chose not to take. Also, look at the two of them in ch. 628, the look they share before going into the other dimension... Some fans are already calling it their honeymoon
For that matter, there's Obito and Naruto. The former tries to pull a We Can Rule Together on him and is determined to break his ideals down since he used to be a lot like him. The Naruto wiki even refers to it as a "fixation".
Orochimaru/Anko; namely in episode 30, where he strokes her cheek!!! Which is VERY creepy... But also kind of cute!