There are a couple of tools that give interesting displays of GO term analyses:

CateGOrizer

REViGO (not a pie chart, but interesting display)

Some truth from the R pie chart man page:

"Pie charts are a very bad way of displaying information. The eye is good at judging linear measures and bad at judging relative areas. A bar chart or dot chart is a preferable way of displaying this type of data.

pie {graphics}

If you are looking for a quick way to generate a pie chart, You can use Panther Classification System for generating such a pie chart. You can either visualize it in a complete/partial ontology level or use your custom gene lists for generating one.

If you need detailed plot using your own data: you can use a generic GO term enrichment tool and then use the ratio of genes - terms to generate a pie-chart using a standard plotting program/tool.