As You Know: When Peter first wakes up sharing Gorbash's body and Melisande calls him "brother," he gets embarrassed and reminds her that they kissed. The kiss did not take place onscreen take place, right before Bryagh knocked Melisande to the ground and grabbed Peter.
Ommadon: I am the world, and the world... is Ommadon."
Badass Bookworm: Peter, who uses scientific facts to unravel Ommadon's magic. His big heroic moment is invoking every discipline of mathematics and science in a Pre-Mortem One-Liner. Never has academia been so awesome.
Color-Coded Wizardry: The four brothers each have an assigned color and element. Carolinus — green and earth; Lo Tae Shao — yellow and air; Solarius — blue and water; Ommadon — red and fire.
Cyclops: The giant ogre whose castle is the gate to Ommadon's kingdom.
He has two eyes, but he used to have three.
Daddy's Girl: Melisande, to Carolinus. It doesn't really become evident until she's in her weird coma, at which point he calls her "my darling, darling child" and weeps copiously. Possibly the most genuinely moving scene in the whole film.
Dangerously Genre Savvy: While initially amused at Carolinus' choise to lead the quest to capture his crown, Ommadon realizes Antiquity must have had a reason and sends Bryagh to deal with Peter.
Eat Dirt Cheap: As Smrgl shows Peter, dragons eat limestone and will swallow gemstones to help digest them, much like birds eat grit to grind their food. Said limestone produces the gasses necessary for them to fly and breathe fire.
Ethnic Magician: The four brothers are oddly diverse. Carolinus is your typical white Merlin-type of wizard, Solarius is an Ambiguously Brown man whose garb suggests Arabia, Lo Tae Shao is Asian (and even has an Asian dragon). Ommadon...well, he's sort of a chalky blue...and hobgoblin-ish.
The Fair Folk: Giles is an elf, but you'd hardly know it from his appearance and abilities; Ommadon also tries to beckon various monstrous fantasy creatures at the climax. The usual small, pretty, beneficial fairy types are depicted early on, though.
Famous Ancestor: Peter is said by Antiquity to be the 777th descendant of Great Peter, who taught dragons to speak.
Fantastic Nature Reserve: Where all of the magic and magic creatures will go to in order to avoid destruction as man increasingly favors logic over magic.
Fantastic Nuke: Ommadon explaining how his magic's influence on man naturally leads to the creation of the bomb.
Getting Crap Past the Radar: At Hell's Way Inn (itself a GCPTR incident), as the humans are about to turn in, Danielle mentions that they may not live to see another night. Cue her and Sir Orrin walking out hand-in-hand, and it's never shown whether they were taken from different rooms of the Inn.
Melisande's recovery from her strange pseudo-coma. Carolinus believes it to have been Ommadon's crown which revived her, having been brought to her by Peter after the battle, adding that her revival was foretold by prophecy. Not only was that prophecy never before mentioned, but if he knew that was the case, why was he so upset when she first went into the coma?
Practically everything about Melisande was handwaved. Who were her parents, who were murdered when she was a child? She's apparently a princess, so how did Carolinus end up as her guardian? Where exactly is the kingdom she's a princess of, and who is running it?
Honor Before Reason: Sir Orrin is adamant about following the laws of chivalry, particularly during his first encounter with Bryagh where he notes it seemed a shame to die over an egg, but he'd already made the challenge.
Improbable Hairstyle: Melisande's long blonde hair is beautiful...except for the part where it looks like she's wearing gigantic seashells on either side of her head.
Kill 'em All: Bryagh slays Aragh, Giles and Danielle, and then Mutual Kills Sir Orrin, leaving Peter alone with Ommadon for the final confrontation. Of course, Death Is Cheap, and they're resurrected when the Magic Realm comes into being.
Knight Errant: Sir Orrin Neville-Smythe. Guess "Sir Brian" was too boring of a name...
Leave Him to Me: A heroic variant. When the group prepares to confront the dragons, Sir Orrin states: "Let me take Bryagh." Of course this is ignored when Bryagh actually arrives, but Sir Orrin was the only one who stood a chance anyway.
Like Brother and Sister: An inter-species version. Melisande, at one point in the film, addresses Gorbash as "brother," presumably because (as Orrin's narration later indicates) they grew up together in the care of Carolinus.
Literary Agent Hypothesis: The main character has the same name as the author of the original book and, for good measure, he mentions in the film that he's writing a book called The Flight of Dragons. As well, the diagram he draws on the stone to visualize how dragonfire works is found in the book.
Peter and Melisande, more or less; their first meeting is pretty fraught with chemistry, and they later share a little interlude the night before he leaves on the quest. This is apparently enough to induce her to follow him into the real world at the end.
On a more squicky level, Sir Orrin decided to marry Melisande on their first meeting...when she was five. Fortunately, this turned out to be more of a case of the knight deciding that he was supposed to marry the princess when she grew up, rather than one of genuine attraction, and he pretty much forgot the entire idea once he met Danielle.
Made Of Shiny: The Silver Owls of the Full Moon; the silver acorn Antiquity gives Carolinus. Antiquity itself, arguably.
Mage Tower: Each magician lives in one which reflects his elements and personality, except Carolinus, who lives in a farm.
This might actually be a bit of fridge brilliance if you think about it. Carolinus is supposed to be the wizard of the green earth, it actually makes sense that he would live on a farm rather than in a tower as this keeps him closer to his element.
Magic Misfire: Carolinus has been doing this more and more often lately, and it's what causes Gorbash and Peter to merge.
Magic Versus Science: The worlds of science and magic are separate dimensions struggling for dominance, although Carolinus admits that science will ultimately win in the end.
Meaningful Name: Sir Orrin explains to Peter that he named the baby dragon Gorbash after the circumstances of his hatching — Orrin had fought with Ommadon's dragon, and it was gory, and he did get bashed up a bit.
Missing Mom/Disappeared Dad: Princess Melisande's parents were killed by "the night demons" when she was a small child, resulting in her being Happily Adopted by Carolinus. No explanation is ever offered for what became of the kingdom of which she is a princess.
New Powers as the Plot Demands: When Ommadon causes Carolinus to lose the ability to track the quest through one magical means, the image of his brother Lo Tae Shao appears and reminds him that Melisande has the previously unmentioned ability to do the exact same thing by entering a trance.
Not Quite Dead: Averted with Aragh. He DID die drowning, but was revived by Solarius, in exchange for killing the Sandmurk queen and joining the quest.
Obviously Evil: Ommadon. While the other four wizards are sagely older men (of various racial backgrounds), Ommadon is a gaunt, hunched, goblin-like creature with yellow eyes, tusks, and even a horn on his nose, to say nothing of his billowing red robes.
Off Model: There are minor animation flaws throughout — e.g. the dragon-rose, described by Peter/Gorbash as "that small golden flower," is quite clearly deep pink.
One-Winged Angel: Ommadon does this for the final confrontation and it ain't pretty.
Our Dragons Are Different: Dragon biology is discussed rather in depth, including their need to eat limestone to generate hydrogen gas, which enables them to fly and breathe fire, as well as their use of soft metal for bedding, as it will not catch fire. This is actually in reference to the Real Life book The Flight of Dragons by Peter Dickinson. In it the author hypothesizes that dragons evolved from dinosaurs, survived extinction by pure luck, and evolved to fly and breathe fire using the aforementioned gas.
Plot Tailored to the Party: Each member of the group overcomes exactly one obstacle. Also, the shield and flute provided to the party by Solarius and Lo Tae Shao each fulfill exactly one function. (Well, the shield fulfills two if you count Peter selling it to the pawn shop guy at the end.) Between this, the Rule of Three entry (a magical quest can't begin without three members), and the beginning of the quest being dictated by Antiquity (itself a vague, intelligent force), it can be inferred that the world of magic is supposed to run like this.
Prophecies Are Always Right: Peter is identified as the Chosen One to Carolinus because he somehow knows what the four magic brothers, Melisande and Gorbash looked like and made them into pieces for his board game.
Rule of Three: When Carolinus first decides to inspire the quest to bring about his idealized magic realm, Lo Tae Shao reminds him that there must be three warriors at the start of a quest, because "the laws so command it."
Time Travel: "Actually, it's been more like ten centuries!"
Title Drop: Not counting the title of the book Peter wrote.
Ommadon: Yes, Bryagh, it's your turn now! You and your legions, attack, demolish, devour, burn, grind them to dust! Go forth and death be thy destination! Doom! Doom! A Flight of Dragons! I COMMAND IT... A FLIGHT OF DRAGONS!!
Token Evil Teammate: Ommadon, the only Evil Sorcerer among the four wizards, which is actually lampshaded and discussed by Carolinus. Subverted in that while he held the position for apparently centuries, early in the movie he goes renegade and becomes the Big Bad.
Wife Husbandry: As mentioned, when Sir Orrin first met Melisande when she was five and he was a fully grown adult he decided he would marry her... he changed his mind pretty quickly when the (also fully grown adult) Danielle appeared.
The World Is Just Awesome: Peter towards the Magic Realm throughout the film, and then subverted in the ending. By denying magic, he sacrifices his only chance to remain there.
Would Hurt a Child: Sir Orrin's first encounter with Bryagh was when he found her eating an entire nest of ready-to-hatch dragon eggs. After he drove Bryagh off, the last surviving egg hatched - into Gorbash.
Wrong Girl First: Sir Orrin's love for Melisande and desire to marry her rather conveniently disappear once Danielle joins the party.