Virgo Shaka awaits for the intruders to the House of Virgo in a Levitating Lotus Position. No surprise here for someone thinking he's the reincarnation of a Buddha. Bonus points for keeping the pose while wearing the Gold Cloth armor of the Gold Saints.
Krishna Chrysaor of Poseidon's Marine Shoguns does the same thing when Shiryu destroys his spear, and he's forced to use his chakra instead.
Fist of the North Star: Ken's rage Toki's "face breaking fist of compassion" attack has him sitting in this position, floating, while using his arms to direct the waves that break his opponents face. Compassionately. The dramatic after-picture has him the same way, but arms in his lap.
Dr. Manhattan in Watchmen does the levitating version of the Lotus Position while creating his fortress on Mars.
Jean Grey, being both telepathic and telekinetic, can do the lotus and float.
Her son, Nathan Summers aka Cable, prefers to do it upside-down.
Leonard of Léonard le Génie encounters an entire squadron (yes, flying in squadron formation) of Tibetan monks flying like this. One even shouts mayday because he has a leg cramp, meaning he can't get the landing gear out.
In B.P.R.D., Liz talks to a Shamgri-La monk while he's in the lotus position three feet off the ground.
R. Crumb's Mr. Natural actually shows some mystical powers by levitating in the lotus position and traveling to the city that way — of course he's tracking down disciple Flakey Foont, who owes him money.
Films — Animation
Gali has a similar pose to this while meditating in the first BIONICLE movie, managing to levitate despite not having psychic powers of any sort, except for telepathy between herself and Takua.
Master Oogway of Kung Fu Panda has an interesting version of advanced meditation: he uses the crook at the top of his walking stick as a place to rest his head, while he balances the rest of his body on top of it.
The Hermit Guru in the Animated Adaptation of Soul Music is in a levitating lotus (with, strangely, a cushion levitating underneath him). He later appears in the Flower Power pastiche, floating over the crowd. In the book it just says he's sitting under a tree (quite possibly a Bodhi tree) with his legs crossed.
In the Rainbow Magic movie, Heather does this. At one point she does it upside down.
Films — Live-Action
The Golden Child. The title character's astrally projected image does this when it appears to Chandler Jarrell.
The first time we see Tom "The Astronaut" of the far future in The Fountain, he is performing the full lotus floating in the air above his small, planetoid spaceship (artificial gravity fields may be assisting him). During the climax, when Tom comes to his personal realization of the ultimate truth of life and death, he climbs out of his bubble-like spaceship (while still enveloped in a smaller, person-sized bubble) and assumes the lotus position again in order to meet Xibalba head on. In the midst of his catharsis, he suddenly appears to the ancient Mayan priest guarding the Tree of Life, who is awed by his presence.
Subverted in God of Cookery when it is revealed that the character has actually left the ground thanks to the security guards who are in the process of carrying him out.
In the Doctor Who New Adventures novel Sky Pirates!, there's a scene where the Doctor's companion finds him "sitting in a lotus and ... levitating three feet off the deck — something he swore blind that he could only do occasionally and with concentrated mental effort, but which Benny had lately come to suspect was the result of being so engrossed he simply forgot to stay on the ground." (They're in a pocket universe with weird physics, which may or may not explain it.)
In the Callahans Crosstime Saloon story "The Wonderful Conspiracy", Jake glances behind the bar and sees that Callahan is actually hovering above the floor, seated in the lotus position. It is one of the first indications that there is a lot more to Mike Callahan than meets the eye.
In the Dragaera novels, Daymar the Hawklord tends to do this whenever he appears via teleportation, or is simply staying still for a while. Lampshaded in Iorich, in which Vlad wonders why Daymar bothers with a feat that's not especially impressive in a society of sorcerers.
Swellhead has Diogenes Club hero of The Seventies, psychic detective Richard Jeperson, come of retirement in the modern era to take on a reality-warping supervillain. In their final confrontation Jeperson gets into this position for a battle of willpower, but not without some assistance from his pretty female sidekick as he's not as flexible as he used to be. The position comes in handy though when the supervillain tries opening a trapdoor to his pit of alligators beneath our hero, who just floats in mid-air. However the trope is subverted because it's the villain's belief in a Worthy Opponent that's enabling Jeperson to tap into his power; not the chanting or Lotus Position.
There's a video on the official web site of The Muppets showing what the character Animal does on his days off. One of the things he does is meditate in the levitating lotus position. The video also includes the "Ohm..." element: Animal's meditation chant is "Wooooomaaaaan..."
The Nali randomly do that in the original Unreal and Return to Na-Pali.
Certain NPCs in Golden Sun can be seen learning how to do this.
There's a mini-game in Wii Fit where you sit very still on the controller pad. If you sit still enough long enough, your on-screen character starts doing this.
This is done epically in the DLC finale of Asura's Wrath by Chakravartin, sitting on top of a nebula, surrounded by galaxies, and casually throwing planets and stars at Asura as he approaches.
In Warframe, Nyx's ultimate ability, Absorb, puts her in that position floating inside an energy sphere while absorbing enemy attacks until she reflects back all damage absorbed.
The introduction of the Monk class to World of Warcraft has also introduced a number of characters that do this. Player Monks even have an optional ability available to them that enables them to use this as a method of flight.
In The Mighty B!, "Dang It Feels Good to Be a Gamester", Bessie hits this sort of zone, where she becomes telekinetic but only for the final level of this video game. She does a floating lotus during this period, then gently drops back down to the floor of the Hive and comes out of the state.
The animated Spirou and Fantasio has two such characters who make several appearances: One is a Magical Aborigine capable of astral projection, and who must tie himself to a rock to avoid flying too high. The other is an Indian scientist who's always about a metre from the ground, possibly even when sleeping.
Sensei of Kim Possible is capable of this, lampshaded by Ron when he uses it to survive a trip over a waterfall. Then parodied when Sensei proceeds to speed around in a display of aerial acrobats that prompts Ron to remark that "Okay, now he's just showing off."
In "Jack and the Monks", Samurai Jack meets a monk doing this.
Several practitioners of Transcendental Meditation have claimed to be able to levitate while in the Lotus position, and there are even photographs showing them in midair in this pose. However, when investigated by the likes of James Randi, it has so far turned out that these claimants merely know how to bounce while in Lotus position, and have somebody take a photograph while in mid-bounce.
Self-proclaimed ninja Ashida Kim has filmed a video where he does this quite unconvincingly.