In "I Was A Teenage Stimpy", Ren is shown with a magazine, and says, "For the adult corn lovers." This was a reference to porn magazines. That, and probably the title card, could've been the reason this episode was banned. In the same episode, it's strongly implied that Ren thought that Stimpy were masturbating in the bathroom.
In "Rubber Nipple Salesmen", there are numerous references to nipples. Also, Ren explicitly points out that the rubber nipples make great "hickies".
In "House of Next Tuesday", it is suggested that Stimpy was wetting the bed (he makes pleasurable sounds).
In "A Hard Day's Luck", a cereal brand is called "Lucky Chodes" (a slang term for penis).
In "Son of Stimpy", Stimpy "gooses" Santa when he was looking for "Stinky".
Some innuendo in some episodes
In "Haunted House", where Stimpy is taking a shower, Ren opens the door and says very cheerfully not to "forget to wash where the sun don't shine".
In "Big Flakes", when Stimpy tells Ren that it was nice for his parents to lend them their cabin for the weekend, he gives a big smile and a suggestive glance.
In "Mad Dog Hoek", when Stimpy and Loaf are wrestling and Stimpy says, "I've come to play with you", we see that Loaf has an uncomfortable look on his face (his eyes go big).
There's some questionable moments with Stimpy and Sven in "Sven Hoek".
In "Pen Pals", Ren mentions getting a Bikini Wax.
In "Haunted House", Ren says, "Let's go up and wet the bed". In the same episode, after the ghost commits suicide, he's reincarnated into a naked man (no genitals are depicted).
In "Fake Dad", Stimpy tells Ren to "be nice to the product of your loins". In the same episode, Kowalski is reading (or attempting to) one of Ren's books entitled "Prison Love".
Some masturbation jokes in some episodes (take "Reverend Jack" for example)
In "Wiener Barons", Stimpy says, "I wish I had a wiener right now".
In "Powdered Toastman", Powdered Toastman's faithful assistant looks pregnant in the beginning of the episode (though her stomach looks noticeably flatter in later scenes).
In the Unedited version of the pilot Ren unknowingly kisses Stimpy (he is disgusted by this).
In one episode, the duo skinny dips without fur (no genitals are depicted). Later on, an equally naked old man (with a small bush covering his private area) joins them in the water; Ren and Stimpy's eyes bob and down as he runs, hinting at them viewing his junk, so to speak. In the same episode, an old naked man appears behind a sign reading "No ball playing".
In another episode where they disguise as babies, the couple and the duo have a community bath (the father removes his robes, we only see his knees, as Stimpy looks up). While in the bathtub with his wife and the duo, the father asks this random guy to hold them while he checks the door, the guy starts whistling a tune looking nervous. The father is outside with another person while a mailbox obscures his genitals (the mailbox opens for comedic effect).
Characters' butts are shown.
In a "Powdered Toast Man" episode, Powdered Toast Man has to save the President who is "caught by my own zipper!" (think "There's Something About Mary").