There are more companies offering services to design and produce a cloudy as software products. I can not say to one another. All seem to produce quality products. I'm not sure what they use as graphics software, but I guess it is something along the lines of Adobe Photoshop, 3D Studio, Micrographix, or something similar.
(1) Killer Covers e-Book covers designed specifically for your product at $117. They also design software boxes and e-zine covers. I recommend taking a look at the samples. Very professional results.
(2) eBook Cover Art This is not software but a service. $99 for a professionally designed e-book cover. Nice graphics but the site is rather unconvincing.
(3).LOOK! JUST 3 STEPS!
1. Load the actions in Photoshop and pull up the basic template.
2. Add graphics and text in your ecover.
3. Click a button to finish your satisfied ecover.
Source: How To Make a Book Cover
Source: Photoshop Video Tutorials