Here are several prototype covers, most of which didn't make it into the final prints of various VeggieTales videos, albums and others.
Where's God When I'm S-Scared? was the only episode whose prototype cover had made it into the final print of the episode. This is the original 1993 VHS cover from the first 500-copies print run, despite Big Idea not having a distributor at the time.
Are You My Neighbor? was the first episode to start the trend of cancelling out its prototype cover before its release. Found on the original 1995 VeggieTunes CD.
Rack, Shack and Benny (found on The Baltimore Sun Wednesday, 29 Nov 1995 newspaper article, Page 167 and The Tampa Tribune Saturday, 9 Dec 1995 newspaper article, Page 144)
Madame Blueberry was originally going to have a similar cover design to the previous nine episodes and distributed by Everland Entertainment just like the early 90's episodes on VHS, but then later scrapped due to a change to the logo and theme song taking place around 1998. (found in Joe Sapulich's concept art portfolio)
2nd prototype cover for Madame Blueberry. (Found in Joe Sapulich's concept art portfolio)
2nd prototype cover for Madame Blueberry in 3D form. (As seen in the actual episode, in the Stuff Mart book)