What's one of Shego's common nicknames towards Kim? "Cupcake." And it seems that it particularly gets under Kim's skin. Considering it's not hard to notice Kim's (lack of) chest size, it seems clear that Shego's rather blatantly teasing our favorite cheerleader about her A-cups.
Shego's line from the beginning of "So The Drama".
"Brain-tap machine ready for prisoner!" "There is no prisoner... Go tap yourself!"
Kim: "So, payback's the sitch!"
Kim: "Careful Bonnie, you know what they do to witches in this town."
In the intro to So the Drama, Ron faces a Sumo Ninja, who speaks with a deep voice. After Kim beats him, Ron gives him a wedgie. At the end of the movie, the Sumo Ninja comes back, looking for vengance... only now, he speaks with a high squeaky voice. That was some wedgie.
In the episode "Exchange", when Ron is attacked by the Monkey Ninjas, he complains "Aww Fu-ji, why is it always monkeys? Why can't I ever be attacked by crazed supermodels?"
In "The Big Job", when Shego asks Seņor Senior Junior why he broke her out of prison, he starts to explain that his father's birthday is coming up — to which she replies: "I don't do cakes... I don't bake 'em and I don't jump out of 'em!"
Clean Slate has Drakken using cue cards to remind himself of the various stages to his plan. When Ron asks why he wasn't told that was acceptable, we get some (possible) Accidental Innuendo with;
Shego: What, ya need a reminder to lose your pants? Kim: That problem has been taken care of. note She's referring to the new titanium-reinforced belt she bought him for their "halfiversary" (dating for six months) which would prevent that problem. Not that she's been helping him lose them or that she dominates Ron.
One could swear that Shego gives Drakken the bird in the episode "The Mentor Of Our Discontent", obscured by a threatening power glow.
Kim Possible lived and breathed this trope. Bonnie was worried in one episode that her boyfriend would be distracted by the jewelry girl's 'Giant hoops'. Rufus has more than a few moments where he represents more than a naked pet. Come on, the writers were clearly in on this and the actors probably spent half the time in hysterics about the innuendo they got to put out on kids TV.
Motor Ed tells Shego that her "chassis" needs some work. Shego gets extremely mad, and he quickly tells her that he was talking about her outfit.
In "Homecoming Upset", Ron and Bonnie end up being the Homecoming Royalty, and are forced to attend a number of events together. At one, Ron is holding a fire hose for some reason, when Bonnie surprises him from behind with a hug. The hoseshoots water all over Kim.
Borderline example from Stop Team Go (as if that episode wasn't laden with innuendo already). When Shego is staying round Kim's house Kim describes it as being 'no trouble, at least until I have to explain it to my parents.' She doesn't say exactly what she has to explain to her parents about the older woman staying the night in the guest room.
The fact it's Shego likely has something to do with it since Kim's parents know who she is. (Near the end.)
Another line from Shego, from the episode where Drakken gets possessed by a pirate's ghost:
Drakken: To the escape pods. And be sure to save my booty! Shego: If I had a doubloon for every time I've done that....
In "Graduation", Drakken's Oh Crap reaction to the Lowardian spaceship hovering over his lair causes his flower petals to suddenlyemerge.
In a Sitch in Time, Ron tries to grab the tempus simia (Time Monkey). Shego catches him and we have this exchange.