Also the Westside Story reference. "A surgeon and a doc above it all."
Rather screamingly lampshaded in the season 8 episode "My Comedy Show", where the new interns are required to do comic sketches about the senior staff for a show. The J.D./Turk sketch? Denise and Sunny pretend to be them. They stare into each others' eyes, and begin making out. When everyone looks around to see JD and Turk's reactions, JD has his arms wrapped around Turk.
Carla:(to Elliot) When Turk and I first started going out, I was afraid he was more in love with his best friend than with me.
Turk: Baby, they've got those lemon biscotti that J.D. loves. Can I have some money to buy him one?
Carla: No, you bought him a present yesterday, remember?
Carla: Alright, let's go... wait, where's Turk? And where's my purse?
In "My Jiggly Ball", Elliot is talking to one of J.D. and Turk's patients:
"Yeah, I think I know this guy. Is he a cocky black doctor with a white doctor following him around and looking at him like he's in love?"
Also from "My Jiggly Ball":
J.D.: I really missed living with Turk, but living with Elliot wasn't that bad.
In "My Last Chance", Denise Lemmon thinks Turk and J.D. are "an adorable inter-racial gay couple".
In "My Journey", J.D. is telling Turk how upset he is that Turk never talks about his feelings, while the patients of the week are an actual gay couple and carbon-copies of JD and Turk.
When Turk shows J.D. the engagement ring he's going to give to Carla:
J.D.: It's beautiful. But my parents will kill me if I marry a black guy
In the Season 8 finale, Carla asks JD whether Turk loves him more than her. She's relieved when she hears it's about equal.
From "My Manhood":
Turk: Dude, we're a little married.
J.D.: I know, and I love it!
J.D. and Dr. Cox
There's also some minor Ho Yay in J.D.'s obsession with Dr. Cox. Here's what J.D. says when during a scene where he's pretending to be him:
J.D.: Now let me get into character. Hating the world... clenching my jaw.... wishing I could love J.D. a little more....
The scene from "My Chopped Liver" when J.D. walked in on Cox's "bi-racial love fest" with one of the interns (not realizing it was just a part of rant Cox was delivering at the moment). He reacted as if Cox cheated on him.
One could also say there's a little bit between Carla and Elliot, though not until later seasons. Carla even once fantasized about being married to Elliot, but so did everyone else in that episode, so that toned it down a little.
Carla and J.D. were the only ones whose fantasy marriages were happy. Several episodes later, Carla plans a perfect bachelorette night for Elliot and exults "We're getting married!"
In the finale, Carla and Elliot try hugging in the style of Turk and J.D. They like it. Carla says "I love the feel of you."
How about Carla teaching Elliot about sex talk, by showing her a porno mag, with a woman with a teardrop tattoo on her bajingo. Elliot asks "Is it sad?" before leaving. Carla says "It does look sad... they always do." Been looking at a lot of them?