Which species were first described by Charles Darwin?
I don't know if these are his earliest descriptions but Darwin did describe several species of Planaria, such as Planaria vaginuloides, P. oceania, plus a new genus, Diplanaria in 1844.

Darwin, C. R. 1844. Brief descriptions of several terrestrial planariæ, and of some remarkable marine species, with an account of their habits. Annals and Magazine of Natural History 14 (October): 241-251, 1 plate.

Perhaps his best known taxonomic work is on barnacles (Cirripedia). He described several species in his monograph first monograph on the group.

Darwin, C. R. 1851 [=1852]. A monograph of the sub-class Cirripedia, with figures of all the species. The Lepadidæ; or, pedunculated cirripedes.. London: The Ray Society. Volume 1

The first monograph was followed by three other monographs on living and fossil Cirripedia. 

I believe that most of his writings after publication of On the Origin of Species focused on expanding his evolutionary ideas rather than on descriptions of new species.

You can read nearly all of Darwin's writings online at http://darwin-online.org.uk. With careful searching you can find all (or nearly all) species descriptions.