As an extremely avid Froyo go-er, I can say that The Red Bench is my favourite in Toronto. The yogurt is organic and house-made, the cookies are delicious and can be made to order, and the staff is generally quite friendly.
Although they don't have a huge selection of yogurt flavours and toppings, the flavours are really good and some of the toppings include their yummy cookies.
They even make ice cream sandwiches with their cookies!
You gotta try this place :)