In some cases I had to crop an image, but then I used a similar image with lower resolution and upscaled it, so that I was able to replace the missing part. It´s pretty fun to find new solutions for different covers. However, sometimes I simply wasn´t able to make a cover I would like to, just because I couldn´t find any suitable resources.
EDIT: It´s always good to have a transparent png of the game title, so that you can cover up the original cover in case you cropped it.
I make virtual DVD cases for my GOG games using mostly the covers on http://www.gogcovers.com
(I like physical game boxes too, but I don't trust the durability of DVD-Rs)
I can do some creative retouching in Photoshop, but for (around) 80 games (not found on gogcovers.com), that's A LOT of work.