Okay, so I organise them all first by the following criteria: I have human man, human female, orcs (which includes goblins), Elves, Tieflings, short races (which is split into dwarves and gnomes/halflings), ethnic, evil and other.
The humans are further split into: Rangers, magic, fighter, commoners, royals, druid, sea faring, shady and knights. This pretty much covers the gamut and most art falls pretty cleanly into one of these categories.
Elves are seperated into: Civilised, wild or Drow
Tielfings are split by gender as are the gnomes and dwarf folders
Evil is any art that looks like it could be used for a villain and is split into: Female, male and "unreasonable" which I use to refer to pretty much any villain that won't talk to the players, so nightmarish monsters and stuff. I feel that this is a significant enough trait that is deserves to get its own subcategory.
Ethnic is of course anyone not overtly white and is split into: African/arabic (basically anyone I would use in a desert setting), asians, americans (so native americans and south americans) and europeans (like very clearly baltic looking or gypsies)
Other contains everything else and is split into: celestials, beastment, bird people (which for some reason I decided to give a seperate category), djinni, dragonborn/kobolds (since some kobolds kinda look like dragonborn), halfies (so centaurs, lamias, mermaids), spooky (skeletons and other monsters that look sentient and not evil), trolls, warforged and then everything else that can't be catalogued.
This system works pretty well for me so far. I also have completely seperate folders for my steampunk and sci-fi pictures that follow the same rules. Whenever anyone asks for requests I can pretty easily follow my tree of folders to find a relevant image.
As for duplicates, I know pretty much everything in my folder so I just don't save a lot of duplicates.