Hi Andrew,
Webwork, which uses GD to generate dynamic graphs, does have a "paint bucket" utility. The graphing category on the Subject Area Templates wiki
http://webwork.maa.org/wiki/Category:Subject_Area_Templates
has several examples
http://webwork.maa.org/wiki/GraphShading1
http://webwork.maa.org/wiki/PolarGraph1
http://webwork.maa.org/wiki/ContourPlot1
and the Index of Problem Coding Techniques
http://webwork.maa.org/wiki/Problem_Techniques
has some (perhaps slightly different and slightly older) examples
http://webwork.maa.org/wiki/DynamicImages3
http://webwork.maa.org/wiki/ContourPlots
The things I use most when writing webwork problems are usually found on the Subject Area Templates page, the Problem Techniques page, and in Davide Cervone's documentation. Usually, google does a good job of finding what you want (e.g., google "webwork filled graph").
Best regards,
Paul Pearson