Why the name 'separable' space?
As far as I know the word separable was introduced by M. Fréchet in Sur quelques points du calcul fonctionnel, Rend. Circ. Mat. Palermo 22 (1906), 1-74. The paper can be obtained via this link (Springer). It's the famous paper in which he introduced metric spaces. He considers first slightly more general objects which he calls classes (V): where (V) stands for voisinage — neighborhood.
Remark: Metrics are introduced under the name écart in no 49 on page 30. It is peculiar that the symmetry condition is not explicitly mentioned but it seems to be understood as Fréchet immediately mentions that metric spaces generalize classes (V) cf. no 27 on page 17f. However, I couldn't find an instance where he actually uses it, he is always careful to respect the order — I may have missed something since I haven't read the paper in detail.
I quote the relevant passage [from no 37 on page 23f]:
Nous appellerons ensuite classe séparable une classe qui puisse être considérée d'au moins une façon comme l'ensemble dérivé d'un ensemble dénombrable de ses propres éléments.
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Ceci étant, nous nous bornerons maintenant à l'étude des classes (V) NORMALES, c'est-à-dire parfaites, séparables et admettant une généralisation du théorème de CAUCHY. Cette limitation n'a du reste rien d'artificiel, elle provient directement de la comparaison des classes (V) avec les ensembles linéaires [...]
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Passons maintenant aux classes séparables. On peut qualifier ainsi les ensembles linéaires en considérant la droite indéfinie comme l'ensemble dérivé de l'ensemble des points d'abscisses rationnelles. Mais il n'en est pas de même pour toute classe parfaite (V).
Below is a translation into English (made by several people here).
Very roughly: Fréchet defines separable spaces as we do it today and says that in the following he will restrict attention to complete, perfect and separable metric spaces. The last quoted paragraph indeed confirms Qiaochu's comment.
We will henceforth define a separable class as a class that can be considered in at least one way as the derived set of a countable set of its own elements.
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This being said, we shall restrict ourselves now to the study of (V) NORMAL classes, that is to say perfect, separable and admitting a generalization of Cauchy's theorem. This limitation has in fact nothing artificial; it comes directly from the comparison of the classes (V) with linear sets.
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We now pass to separable classes. We can qualify in this way linear sets by viewing the indefinite line as the derived subset of the set of its points with rational abscissa. But it isn't so for all perfect classes (V).
According to this part of Hausdorff's collected works, the name "separable" was coined by Fréchet. Hausdorff writes this denotation wouldn't be very suggestive but established. The earliest use in the German Zentralblatt, where the word occurs in a review by Hahn, dates back to 1918. I am sure one can find the first use of the word in the given context in Fréchet's works but I doubt that he will explain his motivation for the use of this particular word there. So we will (presumably) never know...