For Legend of the Five Rings, I took like half the official map (centered around Crane, Scorpion, and Lion territory) and copied it onto a big sheet of paper, in large flowchart-like form. Each point of interest gets its own little location node, making for about 120 locations. I wrote a rough plot outline for each of those, so wherever you go there's something reasonably interesting to do. That's stage one. Here's some of the more interesting ones, basically spoiler-free, since the game might never even go to these places:
In a gambling-based city where everyone wears masks, one of the players is mistaken for somebody else and ends up targeted by assassins.
Rumor is spreading around a port city that the Mantis Clan is press-ganging ronin into their navy, and tensions are high. A ronin stumbles into a tavern beat up, claiming he escaped a press gang. The drunken ronin all start a riot and capture the Mantis embassy. Imperial troops arrive, looking to kill every ronin in the city, including the players.
A bitter student at the Doji Courtier Academy wants to hire the party to get revenge on the most popular girl in school.
A samurai child runs away from his parents to live the ronin life, trying to join up with the players.
The players arrive at the Shrine of Lost Sailors to find it abandoned, with no signs of violence and no convenient journals lying around.
A peasant girl's parents hire the players to escort her to the city to be trained as a geisha by the Scorpion Clan. She, however, would much rather run away with her lover.
The peasants in an extremely superstitious village believe the players to be ghosts when they arrive at the village.