Gemini Rue is probably one of the best game stories I have ever seen. What Joshua Nuernberger did there is amazing. The "twist" that occurs there in the final third is something else. And it's built using AGS.
Gemini rue is one of my favorite games ever, not just point and click.
Another great AGS made game is Technobabylon. That and Gemini Rue are my two favourite Wadjet Eyes Games