The name of the band "New Directions" is a homophone for "nude erections". Made funnier considering Will came up with it whilst in bed.
The same goes for their competition, "Aural Intensity."
Any of Emma's counselling pamphlets:
"There's hair down there?!?!?!"
"I'm still breastfeeding, how old is too old?"
"Help! I'm in love with my stepfather!"
"Me and My Hag."
"Proper Wiping: Easy as 1-2-3." "I Still Breastfeed (How Old is Too Old?)." "My first Canchre." "Why is there Blood in my Pee?" —All from "Naked," Season Four.
The ladies' (and Freddie Mercury's) man Rod Remington. "If I may bring a dash of Rod into this lady-soup..."
In the second episode, "Showmance", Emma catches Rachel in the bathroom trying to throw up. When Rachel informs her that she tried but "I guess I just don't have a gag reflex" Emma responds by saying "One day when you're older that'll turn out to be a gift."
A quiet little exchange in Theatricality
Tina: [referring to her Gaga-esque outfit made of bubbles] My balls keep falling off.
Kurt: I've been there.
The entirety of the "Push It" routine during "Showmance." At one point they were literally dry humping each other.
Santana gets one in "Duets," responding to Brittany saying, "I love your sweet lady kisses," with, "Mmmhmm, it's a nice break from all that scissoring."
Jacob Israel excitedly saying wanky wanky upon seeing Rachel in her revealing attire. As well as Santana beginning the same phrase in response to Carl's "I'm just here to help you fill a hole", before being quickly cut-off by Emma. This is a popular British colloquialism for masturbation, and is quite rude indeed...
When Blaine and the Warblers publicly serenade Jeremiah with "When I Get You Alone" by Robin Thicke, the line "you can keep your toys in the drawer tonight" is kept in. Yeah.
In the history class during "A Night of Neglect," Holly Holiday's "Tomorrow we're going to do Catherine the Great and her pet stallion Fred." For those who don't get it, it's a reference to the Urban Legend of Catherine the Great dying when she attempted to have intercourse with a stallion. In the legend, the stallion's harness broke and Catherine was crushed (in reality she simply had a stroke from old age).
That actually happens twice; Blaine's red jeans in "The Purple Piano Project" were Kurt's in "Born This Way."
Artie: Can't you see [Santana's] manipulating you?
Brittany: That's not cheating either, she told me that.
The word "manipulate" stems from the Latin word for "hand" and its older meaning is roughly "handle or control something with your hand(s)". And Brittany has been known to exhibit a surprisingly advanced vocabulary at times for the sake of Rule of Funny ("mallard", anyone?).
Sue refers to Will's hair as a "head merkin" in "Prom Queen". A merkin is a pubic wig.
Tina denying that rumor about Asian men, anyone?
You know, the one where 99% of Asian men have small penises.
Finn in "Blame It on the Alcohol": "Kurt's been blackmailing me ever since he read my browser history."
The episode 'Blame it on the Alcohol" had a shot of Brittany's bra◊ not on Brittany.
In "Very Glee Christmas", when Santana is sitting in Santa's lap, she exclaims: "Okay, hold on, please tell me that is a roll of Certs in your pocket!"
The lyrics of Brittany's song 'My Cup' in "New York" could definitely be mistreated as meaning something completely other than an actual cup. The New Directions reaction to the song support this with shocked expressions by many of them.
"Sexy" has one between Santana and Brittany with a scene featuring the former fixing up the latters hair, reapplying lip-gloss and cleaning up her disheveled bed as she herself holds a scruffed up hairstyle. Pretty clear to all what just went down before this scene started.
"And so then I told Justin Timberlake, that's not eggnog!" Said by Kurt in the Christmas special.
In universe example, also in the season three Christmas episode: Kurt referring to Blaine as his "best friend and holiday roommate," presumably having fun with the fact that they wouldn't be allowed to blatantly state the true nature of their characters' relationship, while also poking fun at the morality codes of the decades they were imitating.
Sebastian calling Tina "Tina Blowing-Wang".
The football recruiter is named Cooter, which is a euphemism for 'vagina'.
In "I Am Unicorn," Kurt protests at the campaign posters of him riding a unicorn. Santana's response made this troper choke
Santana: In the original, the unicorn was riding you.
"I Am Unicorn" has two more choke-worthy ones:
Brittany: We're going to call it "Kurt Hummel's bulging pink fun-bag".
Kurt when auditioning as Romeo: "Picture it, if you will. Juliet's boudoir, post-coitus."
Schuester rolling over and waking Emma up with "Good morning sleepyhead, guess who woke up just before I did?"
The episode "The First Time", when Blaine and Kurt are about to do the deed, you'll very clearly see a condom wrapper on the floor near Blaine's shirt.
In "The Spanish Teacher", when the group is singing "Sexy And I Know It", Mike Chang gets away with a very provocative move.
To make it even better, then line there is "I've got passion in my pants". Yeah.
Sue's punch recipe in "Prom-A-Saurus" includes "seven tablespoons of Visine, just so we can get out of here in time." Rumoured effects of Visine in a drink include knocking the drinker unconscious (pre-roofie) and giving the person diarrhea. Sue then goes on to suggest Quinn drank the punch, so Finn should check the girls' room.
In "The New Rachel", after Tina says something particularly bitchy, Jacob turns to the camera and says " C U Next Tina!"
From the same episode, Brittany is talking to Blaine at the Lima Bean, and mentions that it's hard to scissor with Santana over Skype.
This exchange between Brittany and Artie in "The Makeover"
Artie: I can be the Cheney to your Bush.
Brittany: I prefer a landing strip.
In "The Role You Were Born to Play", Artie says this when trying to convince Finn to co-direct Grease:
Basically, Olivia Newton-John is strapped to my chest, and unless you co-direct with me, I'm gonna blow her up.
In "Glease", Kitty has this line, complete with a bemused look from Marley:
Kitty: [indicating a miniature toy horse] This is Mr. Jojo. I rode him for six years, until he broke my hymen.
Oh dear god, they did not refer to "2 Girls 1 Cup" in episode 8...
Puck: So I said, you girls are gonna need another cup!
Santana in episode 8, interrupted by Joe:
"And that includes your little hand jive, which to me looked more like a handj-"
Joe: Is there any way Mr. Schue could come back for this?
In "Thanksgiving" the show somehow made it to air with the Warblers performing the song "Whistle", a song about a man receiving oral sex.
When Sue was imagining the cast crashing and burning after their Sectionals loss, she imagines Blaine saying he was performing on the bathhouse circuit. Yeah.
In Sadie Hawkins, similar to Thanksgiving, the show made it to air with the girls singing "Locked Out of Heaven" by Bruno Mars with the line "your sex takes me to paradise" left in.
In "Naked" the Sexy Discretion Shot of Brody walking up to the the dining room table for breakfast nude is a box of cereal called, of all things, Rooster Os. Oh, and then Rachel comes up, gives him a kiss and grabs a banana out of the fruit bowl in front of him, while saying "What?" to Kurt like everything is perfectly normal. At this point, you wonder if the writers were thinking, "Censors, what censors?"
And then it becomes even worse with a conversation between Kurt and Brody about Brody's junk on Kurt's chair...
In "I Do", pretty much all of Kurt/Blaine's scenes. It starts out with a shot of two pairs of shoes intertwined. Then you see Kurt writhing on top of an unknown character (who turns out to be Blaine) in a car. They actually have a closeup of Blaine fisting Kurt's shirt and trying to remove it, and you see Kurt's underwear. Later, they get out of the car and have deliberately positioned their suit jackets over their crotch areas. For a show that mostly depicted the gay couple barely ever kissing, these scenes were quite a (pleasant) shock.
The only thing that was getting Crap Past The Radar was them hiding their crotches after the makeout scene. The rest is the show sticking it's middle finger up at the censors.
Also, it's a Blink-and-you'll-miss-it moment, but you can see Blaine's boxers as he gets out the car as his pants zip is undone. And judging from Blaine's eyeroll as Mercedes catches them making out, this isn't the first time they've been caught...
From "Feud", Sue has an airplane fly over the school with a sign saying "Blaine is on the bottom". Remember that Blaine is gay. Furthermore he claims it isn't true...not really, anyways.
Apparently the original sign was supposed to say "Blaine is a bottom" but it was changed because it was considered too much.
The entirety of Santana's Yeast-i-stat commercial in "Tina in the Sky with Diamonds".
Santana: I want yeast in my bagel, not in my muffin.
Santana acting as Mrs Claus has one. When one kid asks for an educational computer Santana suggests an iPad cause you can't search for porn on the thing the kid asked for.
In 'New New York', Blaine angrily says that the lack of walls in the apartment he and Kurt share with several room mates was a dumb idea because they (in their shared bed) can hear every sound their room mates make and:
Blaine: God knows what they hear from us.
Considering how many blatant references were made about their sex life in that episode, it's not hard to figure out what he's referring to.
On the 2011 Glee Live tour, they pretty much gave Chris Colfer and Darren Criss free reign during the Kurt and Blaine skit (they play two gay characters in an established relationship.) Thus we have Kurt telling Blaine to keep his eyes shut while giving him a costume...
Kurt: Don't look until I say "open them."
Blaine: Kurt, we've been through this.
Kurt: Okay, okay. [To the audience] This isn't the first time we've played dress-up.
There's also Darren moving his face really close to Chris', and saying very sensually:
Blaine: We've been through this. You love the blazer.
Kurt: A lot of people don't know this, but Ontario is my former exotic dance name.
Blaine: (very interested tone) Oh really. How did that work out for you?