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When Crafting a Quest, Don't Start With the Story
"Some adventurers meet by chance at a tavern. They hear about a cave full of gold, guarded by a fire-breathing dragon. They join forces to kill the dragon and get the gold."
This fantasy adventure is a cliche. The players have little investment in the plot. They just happen to be the ones who kill the monster and take its stuff. This is why a quest needs to start with the characters, not the story.
The Characters Come First
Every story needs a central conflict, a conflict that comes from the characters themselves.
Before you craft a plot for a role-playing game, craft the players' characters. In a video game, you (the game designer) will have full control. In a tabletop role-playing game, you (the game master who runs the game) will have to accommodate the decisions of your players.
Craft Character-Driven Conflicts
Make the characters have flaws that lead to conflicts, then craft a story around these conflicts. There must be an external opponent (a supervillain, a demon-lord), but there must also be an internal conflict connected to the external conflict. By the end of the quest, characters must overcome their flaws and their foes.
For example, if a character is a naive young prince, have him betrayed by his power-hungry brother. The vengeful prince must regain his throne while retaining his humanity. If a character is a selfish magician, make him accidentally unleash a terrible demon. The sorcerer must undo his mistakes and learn to care about others.
In either situation, the players have a personal stake in the story because it's their story.
Develop Deep Villains, Not Shallow Ones
Every story needs a good villain, but the best villains see themselves as heroes. They're not just evil for evil's sake. Hitler was a mass murderer, but he thought he was saving the German people, purifying the planet for the master race.
Often, villains represent the dark side of heroes. Batman and the Joker are both costumed lunatics who break the law. The difference is that Batman does it to defend order, while the Joker does it to spread anarchy.
Take these lessons from history and literature. Confront your players with their darkest selves.
Make Sure the Heroes and Villain Meet Before the Final Showdown
In the "kill the dragon" scenario we started with, the characters meet the dragon only when they kill it. Good stories have the heroes meet the villain before the final battle. Earlier encounters establish an antagonistic relationship, resulting in a better final battle.
Be Sure Situations Don't Have Easy Solutions
Pit your players against moral dilemmas. The award-winning "Dragon Age" series forces players to face morally gray situations, like sacrificing an innocent child to save a town. Putting players in deciding roles (and making them face the consequences) increases their investment in the storyline.
Take the Players Someplace Special
Once you have your characters and conflicts, establish a setting. The best settings don't recycle the old "fantasy kingdom" scenario. Try reversing the standard settings (a world where goblins defend their homeland from an invasion of humans) or blending RPG genres (a world where magic-powered robots race to colonize the stars).
Whatever you do, remember that fantastic worlds are nothing without good characters and conflicts. When you keep this rule in mind, you'll create quests that players will never forget.