I used to use a program called "virtual Cover Creator" for windoze and am looking for a similar program from the mac. The software generates 3d software boxes, books etc for display on the internet. You can see an example at http://www.virtual-cover-creator.com
Hey pipermalibu, I personally use this eBook cover Software. Just checked their site, and It's pretty inexpensive at the moment too!
Although it's not a standalone piece of software, it integrates into photoshop and therefore leaves a lot more options open for customising your covers. You can use the tools already in photoshop to make your eCovers really unique. I give it 10/10!
