Five Room Dungeon

One of the best tools I've ever found for designing a side-quest or short adventure is the Five Room Dungeon Model, which I believe originated with John Four's Roleplaying Tips website. In case you're unfamiliar with it, here's the short version:

Room 1: Entrance And Guardian
Room 2: Puzzle Or Roleplaying Challenge
Room 3: Red Herring
Room 4: Climax, Big Battle Or Conflict
Room 5: Plot Twist

The idea is that a good adventure includes an opening conflict, an obstacle that you can't just kill or destroy, a distraction or diversion, a face-off against significant odds, and some sort of twist or link to the next adventure. Its brevity, variety, and focus is actually what makes it so good. Your players don't waste time wandering around fighting off random monsters; instead, each encounter is significant, interesting, and engages different types of players. If you're interested, you can actually download an e-book with 88 unique dungeons built using this model.

While this specifically was written for a short dungeon, it actually easily can be used as an outline for a larger dungeon complex, a major adventure arc, or even a campaign. I certainly have made use of it both for individual adventure locations in my current D&D campaign and the overall flow for the adventure. So if this is something you haven't used before, definitely read the whole article and start using it for your own adventures.