judog1: It didn't take that long compared to some of the other covers I did. I will be posting the PSD as soon as I have settled on a final look. It will be possible to switch between formats (Super Nintendo, NES, N64) and regions by simply toggling groups of layers on/off.
Doom: I based my template on another template - the lower back part was originally of that height. Nevertheless, I do agree it needs to be reduced in size, simply because a lot of it doesn't make sense for Virtual Console games - such as the Dolby Prologic II icon.
The reason I did the Japanese cover first was simply because I like the Japanese artwork best (BTW, I own an European Wii). Like I said earlier, I think it's best to make region-specific covers for each game - for the simple reason that the boxart differs a lot.
For instance, here's a preview of the US version I have been working on...

Notice how the region icon, front of the cover, the ratings icon, and the hue of the picture on the back have all changed. Also, I swapped Link with Zelda on the back.
The game description (IMO) should stay the same for all versions - maybe we should substitute the Super Nintendo logo for a Super Famicom logo for Japanese covers.
BTW, I added Agahnim to the cover because I thought it looked cool. If it's not wanted, I will remove it for the final cover.
As for Thinpaks - you could make your own derivative based on my own version as soon as I have posted the PSD. (ATM it'a mess - about 30MB total, and lots of redundant stuff).