General:
* Marked
* Speckled
* Dappled
* Freckled
* Motley
* Variegated
* Pattered
* Stained
* Dotted
* Flecked
* Sprinkled
For animals:
* Piebald (black and white)
* Roan (mixture of white and another color)
* Brindle (streaks of different colors)
For diseases:
* Infected
* Affected
* Diseased
For other contexts:
* Noticed
* Recognized
* Observed
The best synonym for "spotted" will depend on the specific context in which you are using it.