You have the CDi games...that's not Zelda!
But everything else is good, fine collection you've got. I love the spines on the Gameboy Color Zelda games, are they custom?
I hear you and I understand why many do not include them.
However they are in fact officially licensed Nintendo products despite having nothing to do with the development of them. They even gave the greenlight once the games were complete because even though Phillips was able to use the IP, Nintendo had to approve the final product. If I am expanding outside of the established canon, which I am, the completionist in me demands that they are included. Like it or not, they exist.
Or at least that is how I see it. =P
And yes they are custom replacement cases. I did not design them however. I believe they were based on the original box art so I cannot remember if the actual boxes looked the same from the side or not.