I keep looking at other servers descriptions to see what kind of changes others have made to there server. I have found a fair amount of ideas for my own server this way.
I would say the largest change I have made by work involved was modifying all named mobs spawn chance. I modified most spawns named to have a 80% chance to spawn. I never could figure out a simple quarry to run so I modified each spawn point by hand.
The change that made the biggest change to game play was increasing EXP gain.
you can read all my changes
here