You could try DMDX. This is free software that will run scripts for many different types of psychology experiments. You can google for sample scripts and the Stroop task should come up. The words and colours can be changed easily in the scripts either using text or the new visual DMDX.
Alternatively, you could download the 30 day trial version of Inquisit. There are Stroop scripts for this and these are easy to change. If you like Inquisit after the trial you can purchase it.