Too many to list individually, but they tried to get away with as many innuendos and double entendres in each episode as possible. Kevin Murphy is on record saying that basically the writers wanted both kids and adults to laugh at the same jokes, but for different reasons.
In "The Crawling Eye", Joel asks the bots what they think of the movie. They start talking about human heads and what happens with them when...
Crow: I was listening to the scientists, and they said you had your head up your a-
Joel: *Covers Crow's mouth with his hands*
In The Hellcats, a film with a frankly alarming number of jets of beer foam flying around, Crow repeatedly remarks "I hope that's beer."
In a host segment of Godzilla vs. Megalon, Crow and Tom were looking at some photos with great interest and hide them from Joel.
Joel's riff from Pod People: "Trumpy felt scarred by his ugly hillbilly...nose." A reference to a notorious bit from Albert Goldman's controversial 1981 biography of Elvis Presley. note "Like most country boys of his time, [Elvis] wasn't circumcised. A sensitive adolescent at heart, he saw his beauty disfigured by an ugly hillbilly pecker."
In The Amazing Colossal Man, when the title appears, Crow snarks, "Oh, yeah, you wish!" Then there's this line when Glenn's fiance Joyce is talking to him.
Servo:(as Joyce) I'm still looking forward to our honeymoon!
The writers oftentimes say things like "You can get away saying certain things with a puppet that you couldn't with a person". Notably Crow's "I wanna decide who lives and who dies!" line from Santa Claus Conquers the Martians.
When Tom Servo blocks the hull breach with his hoverskirt, he starts giggling uncontrollably as the vacuum of space sucks at him from underneath, declaring, "I'm experiencing a sensation altogether new to me and frankly, I love it!" When Mike removes him, he growls, "Aw, darn!"
The riffs during a scene involving runaway truck rigs on a hill in Riding With Death, non-stop buttsex double-entendres that get more blatant and dirtier with each riff...culminating in one of the Bots' crack about "...and now, I'll be nudging yer sweet honey pot...", which leads Mike to put the kibosh on the whole thing.
Which of course, leads to this:
Mike: "Drained and satisfied, I'm tracin' lazy circles on yer' supercab now..."
Crow: And you said I was bad.
Mike: Well, you inspired me.
Kevin Murphy's ancient-Roman character whom the Pearl-era Mads accidentally drop in on is named Callipygeas. This isn't a Latin name, it's Greek — and it means "one who has a nice arse".
Before Invasion of the Neptune Men, Pearl is heckled by a Roman citizen because of her lack of popularity in comparison to Bobo, to which Pearl quickly replies, "Slut - I mean, what?"
The Projected Man has a truly volatile one: the lead female actress says "You can't, Chris!" and Servo remarks, "WHOA! What'd she call him?" Say her quote aloud to yourself in a thick British accent to get the joke.
Not to mention a direct mention of the Kama Sutra after a detective states that he's seen a dead acquaintance "in a great number of positions before, but nothing quite like this!"