Gimp is a decent program and is quite capable, but the interface leaves much to be desired.
My program of choice is Pixelmator, an excellent Photoshop alternative. In fact, it is so good, Adobe should be seriously concerned about this program. It can also do vector graphics like Illustrator. It's only available for Apple (both OS X and iOS).
I also use Corel Painter for free hand work, when I want something to look like a painting. Due to a serious lack of artistic training and talent, I don't use Painter to the level that I should.
If I am serious about doing 3D work, I use form•Z-a program I have leftover from a previous career. This is a top-end program and fairly expensive putting it out of the budget of most beginning authors. I mention it only because I use it.
To create a "3D" cover, all you have to do is take the cover image and then use free transform to distort that image. Take an image of a book standing upright, then overlay your cover image on a layer over that. Then move the corner anchors of your cover image until is matches the cover of the book image in the layer below it. On a second layer, draw lines to create a box that would overlay the rest of that book, then hide the book image layer.