Here there be monsters

I think one of the best ways for the DM to make an adventure or campaign unique is through the use of the monsters you throw at your PCs.  Monsters, in my opinion, should not just be thrown randomly at the party.  I'm not saying you don't have wandering monsters.  I'm saying the monsters need to make sense, at least from the perspective of where the PCs are.  Most of the monsters in a normal environment will be similar to each other or part of the same organization.  You won't find a goblin sharing a room with a black pudding for example unless he's some kind of pudding master or something.

Additionally, I think that the DM should consider the following categories when adding monsters to their adventure.

1. Include monsters that are part of the overall campaign thread.  So if there's a githyanki invasion going on that links the adventures together, you should have some githyanki or their agents included.
2. Include that particular adventure's main monster.  If the PCs are in a dragon's lair, you probably need to have a dragon.
3. There should be some common monsters within the context of the adventure.  These are the typical grunts and minions.  In the evil priest's lair, he might have skeletons walking around that guard the place.
4. Lastly, you probably need to throw in one unexpected monster that's included as a set piece to surprise the PCs, while still giving it a reason for being there.