Is interesting how much this is incomplete now and also how difficult would be to update this small atlas having in mind that 1) our generations have a much expanded sense of what fantasy is; and 2) most new places are defended by an army of lawyers.
Racoon city, Matrix, LV-426, Mario island, Nublar, Hogwarts, Irontown, Far Far Away, Gotham...
It was incomplete even for its time, even for titles which were covered. For instance, Dune. Arrakis is covered (as Dune), but not Caladan, Giedi Prime, Kaitain, or Wallach IX, all of which existed in the first two Dune books, which were published before well before the atlas.
I think the only part of Giedi Prime we saw was Pieter's office, the colloseum Feyd-Rautha fought in, and maybe the Baron's chambers? The real action was on Arrakis. I'm not sure the topology of all these planets was really dreamed up until the son took over.
I've always wondered what the large-scale map of the Dune universe looks like, at the planet and system level. Although it really doesn't matter, with the Spacing Guild and it's navigators. Space becomes somewhat meaningless when you can bend it.
It's not really clear exactly how folding space works, though. Later in the series, no-ships are used and one of the reasons they can be used is because they can calculate how to avoid interstellar objects just as the Guild Navigators do (which I believe is not mentioned until the moment the no-ships are actually introduced).
So even with foldspace, actual positions may be useful, although I don't think these are discussed much in the novels, so I supposed there's no real basis for a map.
Which speaks to the GGP's comment about many more things being considered fantasy. City 17 exists on an alternate Earth and there are countless alternate Earths in fiction. The first two that come to my mind are the Fallout universe and Philip K. Dick's Nazi- and Japanese-occupied United States.
Racoon city, Matrix, LV-426, Mario island, Nublar, Hogwarts, Irontown, Far Far Away, Gotham...