I've been there twice on day trips. Here are some of my favorites that have not been mentioned yet.
Bell Tower in Market Square - there are 366 steps and the ones toward the top are narrow and winding. You also have to slink up against the wall since there is not enough room for guests to go up while others are going down. The view from the top is amazing. It is VERY noisy when the bells are ringing.
Church of Our Lady - this church contains a Madonna and Child by Michelangelo. It was removed by the Germans near the end of World War II, found and returned several years later.
Memling Museum - there are a number of nice museums. We chose this one because I was interested in the fact that it had been used as a hospital.
Groeninge Museum - we wanted to go there, but it was closed to change over an exhibit. It features early Flemish art produced in that area.
Bruggemuseum-Gruuthuse - this was a wealthy brewer's home and had a little of everything.
I was not aware of any mark to tell which shops made their chocolate on site, but we actually saw it being made in the shops we got chocolate at. We were lucky to have a Belgian foreign exchange daughter, who told us which ones to go to.
Dumon Chocolate shop - the shop looked like something out of a fairy tale, with gingerbread walls and an impossibly small door. When you get up to it, you see there is actually a little landing with a few steps down, so the door only looks too small.
Madame Dumon herself helped us to pick an assortment of chocolates (handmade by her family) at the shop.
Chocolatier Stephan Dumon - another shop owned by the Dumon family. The outside of the building is old, but inside it's a mix of modern decor, sort of Art Deco design and less traditional chocolate than at the other shop. You can see into the very modern kitchen (they were not making chocolate at the time we went - kind of late in the day). We were told to go there for the "best hot chocolate you will ever have". I won't spoil the surprise about how it's made, but I will say it more than lived up to the hype.
The Chocolate Line - in this shop you could watch chocolates being made through a glass window that overlooks the kitchen.
Belgian waffles - enough said.....mmmmmmm!