The second Shawn turns up, Cory basically forgets that he's married to Topanga - Some things never change. This is lampshaded by Maya and Topanga during "Girl Meets Home for the Holidays."
Lucas seems to like Farkle quite a lot. He's always saying nice things about Farkle. Lucas also goes out of his way to make Farkle feel good about himself. Farkle is also a loyal friend to Lucas and is in Lucas' words the "best friend he's ever had!" Also Farkle keeps Lucas up at night. Ok boys just ask each other out already!
Let's not forget this gem in "Girl Meets The Rules":
Lucas: [to Farkle, in a predatory voice] I'm hungry. Farkle: What do you mean by that? Lucas: Nothin'. I'm just...really hungry. Farkle: Because...we're best friends??? Lucas: Yeah. You know what else? *serious tone* I don't think I've ever been this hungry...
Zay seems quite attached to Lucas as well, even (falsely) claiming he followed him all the way to New York. In addition, we find out the Lucas's past violent actions were all to protect Zay.
Farkle and Zay even fight over who Lucas's "best friend" is.
Rosie McGee's attempts to befriend May Clutterbucket in "Girl Meets 1961" have more subtext than was probably intended. Rosie watches May from across the club and writes about May in her journal before sharing a look with her across the crowded room, which could be platonic enough. However, Rosie then introduces herself with the (essentially a pick-up) line "You are really interesting-looking. Are you as interesting as you look?", makes a big deal of choosing to sit with May instead of anyone else in the club, and calls May beautiful after her performance. Not to mention Rosie continuing to write about May long after May abandoned her and naming her granddaughter after the last place she knew May was heading…
When Maya complains about wanting a back rub in "Girl Meets The Forgotten", Riley happily volunteers to provide one. Maya then responds that she doesn't like Riley's back rubs, since it feels like spiders running up her back, and Riley then tries to convince her to let her do it anyway.
Just Riley and Maya, full stop. Cory and Shawn at least waited a few seasons, these two act like they're already married from the get-go. Hell, the fans have even said that if GMW aired on Freeform Riley and Maya would get together.
They constantly hold hands, have absolutely no personal space around the other, and are practically joined at the hip. In one episode, Auggie amusingly remarks that Riley and Maya will get married (and it's worth noting that nobody bats an eyelash at this). They also seem much more touchy-feely with one another and always seem to gravitate towards the other regardless of who's in the same scene. Granted, girls are generally much freer with physical affection between themselves than boys are, but Riley and Maya pretty much act like a couple (in the best possible sense), just minus kissing.
Not to mention how often they parallel the canon couples, especially Cory and Topanga. Riley even goes so far as to compare their relationship to her parents', calling Maya her "extraordinary relationship".
At one point, Riley worries that when she and Maya get boyfriends, they won't love the boyfriends as much as they love each other. Maya declares that they'll just love their boyfriends in a different way.
Riley: What different way? Maya: Less.
There's that part in "Girl Meets True Maya" where Maya is at the park (a park that has a memorial in support for LGBT people, no less) at night, one of the bad girls whispers seductively into her left ear. Oh, how subtle.
