In a student election, Jerry tells everyone that Milton doesn't shower after gym class. Milton confides to Julie that it's because the water is cold and there are boys in there.
In Kim of Kong Milton plays the part of a jilted lover when he finds out Kim's been sparring with Jack: "Please don't tell me you sparred (slept) with him! Here! On our mats (bed)!" (Milton runs out of the room and reappears a moment later, drowning his sorrows in ice cream) HOW IN THE HELL DID THAT GET OUT?!
When Rudy meets the woman dressed as a cat he tells her he knows a lot of knock knock jokes. The woman tells Rudy he should start knocking. The look on Rudy's face just sells it.
In Reality Fights, Jack gets hit by a tennis ball. The fact that he was clearly in pain and his voice became high-pitched should be a good indication of where he got hit.
In New Jack City Milton wanted to have a piggy back race with Kim and Carson, so he jumped on Jack's shoulder and smacked Jack's butt onscreen.
Jack:Did you just-
The episode Kickin' it Old School Rudy asks the teacher if he can clap her erasers.Also, the apple eating scene.
I'm pretty sure Rudy tried to jack off a bull in Witless Protection
In "Eddie Cries Uncle" Jerry tries to adjusts Eddie's balloons and Eddie tells him to knock it off or they'll pop. Keep in mind that during this moment, Eddie is disguised as an old lady so the balloons are basically fake breasts. When Big Easy hugs him, the balloons pop.
In "Witless Protection", Rudy says his finger has two purposes: the first is to point at criminals and the second he doesn't feel comfortable saying it in front of the cop.
In another episode, Jerry thinking an old lady is Rudy disguised, asks "him" if he wants to "lie on the mat and sweat a little". The lady then hits him with a tray.
Probably the most obvious and literal example so far is the duck poop storm in "Jack Stands Alone".
In the second episode, Jerry and Jack smack their school's sumo champion janitor's butt while he's wearing nothing but a sumo diaper.
Jerry and Jack: *at separate times* Whoa, skin on skin. *singsong* Awkward.
In The Wrath of Swan Jerry says he was going to the dance because Milton paid him $60 and let him see his turtles go at it
Also Frank thinks that because he and Kim now share a locker, he thinks their married now. Take that however you will.
In Nerd With a Cape Jack says that Milton's superhero costume is pretty skin-tight, so skin tight that he can see that Milton had two carrot sticks and a meatball for lunch, and Jack is notably looking down at Milton.
In the episode preview for Invasion of the Ghost Pirates the announcer wonders if the ghost pirates are after some booty, cue a clip of Rudy pulling up his pants to show off his not!shapely ass and asks if Jack and Milton have ever gotten a load of it.
In the episode itself, at the end the real ghost pirate wins a carnival prize and says he wants the giant banana, and let's not forget Rudy constantly calling himself "ghost candy".
In Capture The Flag Claire from the rival private school catches Jerry in the hall of the school and says she knows why he's there, to take something he wants. While flipping her hair and flirting with him like mad.