Namely fimfiction.net. A good portion of the fics there have cover art for them. Ex:
http://www.fimfiction.net/story/8933/ and
http://www.fimfiction.net/story/2766/.
I have played with Generate Cover a little bit, makes adding the word 'Complete' in the center of every cover for completed fics a snap for Nook browsing.
Your new EpubMerge plugin looks great too; I will need to remind myself to only use it on the device however.