I enjoy the occasional personal tweak, so maybe we can share ours here?
1) e.g. bright stuff hurts my eyes, so I made 'cloudy day desert' tiles.
[Edit]I notice a lot of tiles still are using oldschool single-layer technique. E.g. a cactus on the desert also has the sand around it, it's not a seperate sprite on top of a stock desert tile. This saves some execution time in software rendering, but makes the graphics assets work a lot more time consuming to change.