Téa: Wow, look at all the phallic imagery! (montage of monsters growing horns, getting existing horns enlarged, and a knight with a long hard cold lance) Joey: What're you talkin' about, Téa? There ain't anything remotely suggestive about this duel! Yami: Now watch as my mighty lance penetrates your moist cocoon!
In The Dirty Pair: Dangerous Acquaintences, Kei and Yuri are on vacation on a non-United Galatica planet. They see an attractive guy and start talking to him:
Kei: Oh look… a train! Gee… I jush love watchin' a train enner a station… don' you? It reminsh me of someth— ?!
But right then, Kei sees that a wanted criminal who she has a grudge against is boarding the train, and runs off in pursuit.
Empowered has some example. Look at Thugboy and his gun at the cover of #1.
In a For Better or for Worse strip set during Michael's early teenage years, his friend Gordon has what he calls "hormone attacks", where anything that could be taken as sexual causes him to pass out. When their gym teacher holds up two basketballs at chest height...
Another, single-panel gag has the memorable line from his little sister Liz, as they both cloud-gaze, "I see Mickey Mouse['s ears] in the clouds...what do you see?"
The alien squid in Watchmen (the comic version) vaguely resembles a woman's crotch, legs spread. Because the resemblance is vague and grotesque, the squid is dead, and there are also a lot of dead human bodies lying around, this is also a case of Fan Disservice.
Dan and Laurie fight off a gang of muggers. Their actions afterward are to stand there panting and sweaty, briefly look at each other, and then look away, whereupon one of them lights a cigarette. Sadly less obvious in the movie, thanks to the removal of Laurie's smoking.
When Dan and Laurie have sex in Archie, the flamethrower goes off at the climax.
X-Men 15, “Prisoners of the Mysterious Master Mold!”, at those long gone days of Stan Lee and Jack Kirby. The X-Men need to hold on a platform to ram into a building, and Iceman couldn't craft anything better than a surface with a pair of phallic cylinders to hold. See here
Beast: This doesn't seem very dignified, but I suppose it's necessary.
Film (Live Action)
Office Space does this when Lawrence is talking about how he'd do two chicks at the same time: He's sitting down and holding his beer bottle against his crotch.
The third Pirates of the Caribbean movie had Barbossa banging on a table with a chain shot (two cannonballs connected by the chain) for emphasis. Later he stands up and we have a perfectly framed shot of his legs, with the two cannonballs dangling in between.
Jack: Whose boons? Your boons?
Also, the scene with the telescopes.
In Austin Powers: The Spy Who Shagged Me, there's a scene where Austin and Felicity are packing and unpacking inside of a tent, but to the horrified soldiers watching outside, it looks a lot different...
The scene is repeated in Goldmember, where Mini Me first acts as a prehensile wang and then a demonic birth.
The opening scene of 1941 where a skinnydipping woman finds herself clutching the upthrusting periscope of a surfacing Japanese submarine (also serves as a hilarious Jaws take-off).
This is also lampshaded. "In position under enemy scrotum!"
In Airplane!, the stewardess must inflate the automatic pilot by blowing into on a tube on his belt buckle... when someone looks at her from behind it looks like fellatio. The effect is only accentuated when Otto (the automatic pilot)'s previously bland and stoic expression changes into a big, wide-eyed grin once she's finished...
In Bridget Jones' Diary, Bridget's mother gets a job shilling an "As Seen On TV" gizmo at the mall. It automatically shells a hard-boiled egg. Just put in the egg, then work the shaft and out pops an egg! Then some white liquid.
Blazing Saddles had the Governor trying to put a pen back into its holder. Hedley Lamarr just tells him, "Think of your secretary," and he gets it right into the little... place it's designed to go.
Dr. Strangelove, filled as it is with weird sexual innuendo, starts with a scene of two airplanes refueling in midair, but the way it's filmed makes it look like they're having sex. Which was brilliant, because the footage was not shot for the movie: it was Stock Footage. All Stanley Kubrick did was play an instrumental version of "Try a Little Tenderness" over it.
In Down with Love, two characters are having a phone conversation at the same time as engaging in various activities. A split screen makes these activities simulate sex. For instance, when the man is on the top of the split screen, he is shown doing push-ups while the woman is on her back on the bottom of the split screen. They even simultaneously have a "post-coital" cigarette at the end of the scene.
In Rear Window, Jeff is spying on his neighbors with binoculars. Frustrated when he can't see enough, he puts them down, and picks a camera with a telescopic lens. As in. . .longer. Classic Hitchcock symbolism. Oddly, despite the fact that voyeurism is generally a sexually deviant activity, this isn't why Jeff is snooping.
A much darker example in Psycho during the infamous shower scene. The knife has a distinctly phallic silhouette, the stabbing that represents penetration, the ejaculatory spurts of blood—the whole murder is symbolic of a rape that the severely sexually frustrated and repressed killer cannot otherwise carry out.
Most likely an accidental version in Man of Steel; the pods that Zod and his followers are encased in for transport to the Phantom Zone look an awful lot like enlarged dildos when viewed from beneath.
The Wallace & Gromit movie has Totty standing behind two chest-height watermelons, just as she says that her suitor has never taken interest in her produce. A similar sight gag happens when one woman holds up two bitten brassicas (a sort of cabbage) which have been "ravaged in the night."
Not to mention a naked Wallace in a box with the words "May Contain Nuts" on it.
Kronk's New Groove features a scene where he and his love interest bake bread, which turns into an extended dance sequence. Which includes a shot of Kronk behind Miss Birdwell and... um... helping her knead bread dough.
The Old Spaghetti Factory serves the Meat Lover's Treat: a plate of spaghetti with Sicilian meatballs and a whole Italian sausage.
Several French restaurants have independently invented a dessert called Rêve de jeune fille ("young woman's dream"). It's made up of two spherical scoops of vanilla ice cream with a peeled banana standing right between the two. For additional naughtiness, serve with cream on top of the banana. For additional naughtiness, serve without a spoon.
Terry Pratchett does this with landscape in Lords And Ladies. At one point, Nanny Ogg and Casanunda have to visit the Long Man, three large burial mounds in the forest. One long with two round ones at one end.
It also gets one of the heaviest lampshades possible.
A Wizard's staff has a knob on the end.
In Unseen Academicals, Glenda points out to the wizards that with the placement of two large letter U's on their uniforms, they'll "look like they've got bosoms!"
Live Action TV
The Whedonverse has a lot of these. The stake in Hush, Wesley's arm-blades in Spin The Bottle, and Buffy (hilariously) crushing Warren's *ahem* magic orbs.
In the episode when Buffy discovers her post-Angel rebound guy Riley at the vamphouse, the scene opens with him and a female vampire kneeling before him, shot at an angle (and with sound effects) that makes it unclear just what she is sucking, but that there is definitely sucking going on. Then the camera pans around to show that it's just blood from his arm.
Not to mention Buffy's erotic dream in the Season eight comics, where she's in between Angel and Spike and all around them are gushing volcanoes, trains entering tunnels, stakes, flowers.. you name it that panel had it.
An accidental version occurred in the third season of the UK version of The Apprentice, where one of the contestants had to sell a trampoline on a shopping channel. It might be a bit NSFW.
This made the "The Apprentice: The Worst Decisions Ever" special.
Simon: It's not my fault. I'm innocent. Everyone else, out there, are the dirty-minded ones. I can only attest to being an innocent person.
The design of the building in this clip also qualifies. Yes, that's the same candidate.
In one of the episodes of Samantha Who, the title character (who has experienced amnesia) is trying to remember what sex is like and the next scene shows her boyfriend repeatedly putting a pencil into a mechanical sharpener.
In The Stand, Larry is trying to get some gas and gets Nadine to help put a hose into the floor as they talk about how Joe needed a surrogate father as well as Nadine. They feel very awkward as they realize the symbolism here.
In Robin Hood, Little John totes around a large staff, and in the episode Treasure of the Nation, meets one of the Queen's bodyguards, who has an even bigger staff, with a large wooden knob at the end of it. Little John spends a good part of the episode eyeing it nervously.
The Benny Hill Show has several sketches where Benny is a gardener watering plants with a hose held up at crotch level. It's placed so that you don't see the hose at first, just the water coming out.
A frequently-run ad for Andromeda has Dylan Hunt using a force lance, a laser-flashlight that expands into a six-foot staff. He holds it right at crotch level, in profile, and lets it grow. Seriously, I'm amazed it even got on the air in prime time, let alone run all day when kids could see it.
The Media Watchdogs descended upon the Super Bowl XLI halftime show, when Prince played his guitar (shaped to look like his symbol) behind a drape in silhouette, making it look as if the neck is...well...and oh, yeah, a piece of the body stuck out below the neck to look like...oh my.
It's Prince. The man could do his taxes with an abbacus and make it look sexual.
In Life On Mars, Gene and Sam are visiting a comatose girl in the hospital when they start a fight. They whale on each other for a bit, and then the camera cuts to them sprawled on the floor at the end of the bed, slightly the worse for wear, breathing heavily, and with Gene smoking a cigarette as they have a heart-to-heart conversation.
In Glee, when Emma is singing about how she could have "done a thousand things I've never done before", there's a close-up of a pearl necklace. For those who don't know, it's a slang for when a man ejaculates semen around the other's neck.
The music video for Devo's "That's Good" has a bluescreen background that, on occasion, shows a french fry going into the hole in a donut, followed a naked woman from the shoulders up writhing in ecstasy. It's...fairly unsubtle. (Then the fries start breaking as they go in, and the woman begins looking downwards with a sigh of frustration...) MTV refused to air the video before either the french fry or the donut was removed.
Queens of the Stone Age's "Go with the Flow" video has lots of visual innuendo tucked behind the more overt examples.
Exterminatus Now has one strip early on where a beam sword (think lightsaber) is held in front of one guy's crotch and activated, as two demons shapeshifted into scantily clad women make out in front of him.
Superdickery.com has an entire gallery of such things, starting here.
In Chapter 10, Act 2 of the web animation series Broken Saints, when Sandra talks about wanting to do field work at a naval base with hunky sailors, a little animation features her moving her pencil to and from her lips. It's not much, but its been confirmed by Word of God to be intentional.
In the Looney Tunes short "Russian Rhapsody" when the gremlins make their entrance a fat one stands near the edge of the plane engine and another gremlin's very long nose pokes out from between his legs.
In an episode of the Simpsons set in Washington D.C., they visit the Washington Monument. Marge giggles and whispers something in Homer's ear.
Homer: "Oh, Marge, grow up!"
Avatar: The Last Airbender had a rather infamous scene that implied Sokka and Suki were meeting up for a romantic night in his tent, and the next morning Sokka is seen wearing a flower necklace. In other words, Sokka got lei'd and Suki got deflowered.
To clarify, the ash piles are the Dwemer themselves. They all died rather...suddenly.
Skyrim adds Haelga to this list of... *ahem* yeah. In her bedroom, there are manacles above the bed, stamina potions in the shelves, leather strips on a table, a copy of the Rated X play script for "The Lusty Argonian Maiden" on a nearby nightstand... Bethesda one-upped themselves this time.
In Snatcher, Gillian sees an underage girl in his apartment, using his shower. She freaks out and sprays him with her showerhead. He spends the next scene looking damp, flushed and shocked with fluid dripping down his face.
In No More Heroes, the main character Travis recharges his Beam Katana by shaking it. But, the behind the back camera makes it look suspiciously like something else...
The Grand Theft Auto games... for example, practically any bowling-alley you can find, will have a sign prominently featuring two bowling-balls and a pin.