I have a polygon shapefile and I want to generate a table of a count for each pixel value in each polygon. My main goal is to find out what pixel is most abundant in each polygon. I am using ArcMap 10.
Focusing on your main goal, simply compute a zonal majority of the value grid, using the polygons for the zones.
If you still want a count of each unique value within each polygon, provide the polygons with unique identifiers, convert them to a grid (having the same origin and cellsize as the value grid), and combine the two.
These operations require the Spatial Analyst extension.