I don't own a Virtual Boy, but it seems to me that UGCs would be way too big, and waste a lot of space. I would stick with the DS cases (NOT 3DS cases) and modify them. Modifying cases can suck, but the VB library isn't that large, so it shouldn't be too time consuming. Plus, the artwork is ready to go.
I know that a few people have bought red DS cases for their VB collection. I think that would look pretty cool on the shelf.