I've been quite interested in the idea of both WiiWare and Virtual Console games in their own DS cases for a while, so here are two basic ideas I've put into the concept.
The first is this basic design for Virtual Console game covers.

The concept here is very simple: an uncomplicated design that is easily and readily distinguishable as a Virtual Console theme at a glance, laid out above the original game's boxart. The purpose is easy creation of VC coverart; just grab the original cover, resize it, make a spine, and slap on the banner. Of course, this idea is far from perfect and desperately needs tweaking. The current layout is for horizontal covers, which is just peachy for SNES and N64 games. Wouldn't be too difficult to modify it for vertical covers, rotate the strips so they're running down the side on the face of the box instead of along the top, but I imagine those red Genesis cases would look pretty silly wiith that on there. Moreover, I don't know what would be done for Game Boy games and the like, those kinds of covers that are already on the site in DS case styles, for the 3DS VC. But of course, this is still just an idea, and hopefully something can be figured out that would work across the board. Remember, though: the main thing is to be able to easily convert coverart from the originals to the DS style.
The other idea I've worked on is fitting SD cards into DS cases. This was what I had in mind.

This is a Gamestop DS case that I had previously cut up to fit a Game Boy game. I made one more little modification to the DS card slot. I cut out a piece of the inner "wall" of the card slot, on the bottom right. The effect this has is that I can fit an SD card case into the DS card slot.

The cut was sloppy, and the piece of wall remaining on the right is loose and floppy because I cut too far in so it's severed from the bottom wall, but the result is a surprisingly snug fit. When it's closed, the SD case doesn't move around at all, even when I turn it upside down and shake it as hard as I can. And this is with the top half of the DS card slot missing, and only a tiny piece of plastic supporting the entire right side. The SD case does pop forward out of the slot without much difficulty, so it's still liable to fall out if you open the DS case if you're holding it vertically when you do so, but since the card itself is in the small SD case, there's no danger of the contacts becoming dirty or damaged or anything if it falls. The SD case itself presents a slim enough profile that the DS case has no trouble closing, and it doesn't bulge at all.
What I like best about this setup is that, since it uses the DS card slot, it can be done with eco cases - so you don't have to sacrifice any GBA slots for it - and even 3DS cases if I'm not mistaken, which work well with a WiiWare/Virtual Console theme (as demonstrated by the enigmaxtreme's Cave Story mockup, as well as my Super Metroid mockup) Again, though, still just an idea which may be improved upon. Lemme know what you think of my ideas. Tell me why they suck, but more importantly, things that might be changed about them so they won't suck.