A few general guidelines for finding a store in your area: Depending on where you live, try
upscale toy or game stores in the malls in your area
specialty stores that cater to frisbee golf, kites, juggling, or magic supplies etc
some hobby/craft stores also carry them
National chains like Walmart and Target are now known to stock YYF, and Duncan lines at some locations.
As always, call before you go to make sure that they are still in business, or have what you are looking for.
So, rather than the herculean task of maintaining a directory of all brick and mortar stores (in the world? in canada? in the us?) that carry yo-yos, I think it may be better to refine the above strategies for figuring out where yo-yos are likely to be in your area, and always, always calling first.
I also made the directory post a wiki so users at trust level 1 and higher (read: users who hung around and spent some time reading topics after signing up) can edit it.
If you know of a store that carries yo-yos near you, and is not part of a larger national chain that is already known to carry yo-yos feel free to edit the directory post.
Major to @jhb8426 for carrying this forward for almost a decade and keeping it up to date.