My favorite is caramel apple, covered with white chocolate and rainbow sprinkles.
As for a wait, I've never had one. Granted you have to wait for your food to be made, but I generally go during the day, night might be more crowded. Since I"m a teacher I normally go on the busiest weeks/weekends, too!
The location is downtown disney. Goofy's Candy Co is located near the Rainforest Cafe. If you enter in building through the main entrance, go straight until you hit the refridgerated glass. Bear to your right and there will be forms to fill out. You can then watch your food be created right in front of your eyes.