Here's a short list (I have two main fandoms, so this shouldn't take long)
-Yukio Oikawa and Hiroki Hida: Yukio's soul-crushing obsession had to be more than simple friendship, even if Hiroki considered him 'just' a close friend. I don't think he really knew, though, just how much Yukio *needed* him...
-JP Shibayama and Zoe Orimoto: Well, it's even canon on JP's behalf. I suppose I think Zoe needs someone smart, witty, and fun, and JP is all those thing and more, and he'd be more than willing.
-Takuya Kanbara and Kouji Minomoto: Takuya gets to the train station in the first place because he's following Kouji, who he's never met. No reason is ever given. Also, he gives more consideration to Kouji than anyone else (and he highly regards his teammates, so for him to give so *much* more notice to an individual is something that raises an eyebrow)
-Matt Ishida and Tai (uh...whatever his last name is this week): They fought, they held hands and got hit by 'love arrows', they fought some more, they bonded, they fought, and had they had DNA Evolution in season one, you just *know* they would have been stuck with each other.
-Takato Matsuki and Jeri Kato: When you go into the depths of a raging delete progam gained sentince to rescue a friend, it could be platonic. When you cling onto each other for that long, it's a bit more.
-Mitsuo Yamaki and Reilly Ootori: If it wasn't for her, he would have died in the collapse of the Hypnos building, or wound up in a padded cel someplace. She showed him that life was for more than order, and that sometimes it's nice to be yourself, even if that means letting some chaos into your life. Just as long as it's not the D-Reaper, that is.
-Jesse/James: Yes, I like this. I like this a *lot*, even though I don't actually think it will happen until later. They're the best of friends, and will do anything for each other (although they will deny it). Not to mention that they kind of *have* to end up together, as they're the only people who can stand to be around each other.
-Morty/Eusine: A little on the obscure side, as Morty was only in three episodes and Eusine was only in one (...and the Raikou special, but he was rather...different in that. That's for another time, though, if you really want me to say how, I'll put it in a reply). But in that single episode--"For Ho-Oh the Bells Toll"--we see a lot about the two of them. Eusine's vaguely self-destructive obsession with capturing the Legendary Dog of the North Wind has taken a toll on Morty, who regards him with longing glances and a sort of defeatist resignation (translation--Morty spends the entire episode acting like a jilted lover).
-Oak/Delia: A scriptwriter said that Oak "takes care of Delia like a daughter". But you don't get embarassed to go to the beach with someone you consider your daughter, wise guy. (scene referenced is in "Beauty and the Beach" when Ash asks Oak "Why are you here with my mom?" Oak gets flustered and immediately changes the subject, which remains unanswered)
-Giovanni/Domino: Some may say this isn't obvious, but I saw it as such. She's very casual around him, despite the formality of pretty much every other agent. She's allowed to talk back to him, call his private line (something he's yelled at JJ&M for), and attempts to act as a voice of reason. He wouldn't take that from just anyone, you know.
...wow, 3:35 already? I have sleep to get!