I'd say, looking at your most recent covers, it's mostly dust removal and logo replacement, Finer details.
Contra 3 has some dirt by the "The"
Fallout 3 - The contrast/ brightness was boosted a little too high, the grey rings on the front Xbox 360 banner are gone.
MegaMan 8 back cover- has some dust on spines, ESRB, and SKU. A good way to clean up the SKU is to take a bit of the lines towards the bottom and stretch it upwards.
Red Faction, some dirt on back, the Copyright text is a bit blurry, a good way to sharpen it, with white text on black or vice versa, is to desaturate it and up the contrast.
Spirit Camera - Dirt above logo on front, spine, among other places, Cover seems a bit dark, relapse the Seal on the back, Nintendo, 3DS logos. Desaturate the grey text, it is a little off color, and sharpen.
Kirby Super Star - forgot to remove a layer in template on back, higher contrast on back, Spine drop shadow.
The DS template could use some work as well, I was working on a updated GB template at one point, I'll get to DS sometime soon.