It seems reasonable to me that in operator theory the term "spectrum" comes from the Latin verb spectare (paradigm: specto, -as, -avi, -atum, -are), which means "to observe". After all in quantum mechanics the spectrum of an observable, i.e. the eigenvalues of a self adjoint operator, is what you can actually see (measure) experimentally.
Edit: after having a look to an online etymological dictionary, it seems the relevant Latin verb is another: spècere (or interchangeably spicere)= "to see", from which comes the root spec- of the latin word spectrum= "something that appears, that manifests itself, vision". Furthermore, spec- = "to see", -trum = "instrument" (like in spec-trum). Also the term "spectrum" in astronomy and optics has the same origin.
In algebraic geometry, I believe the term "spectrum", and the corresponding concept, has been introduced after the development of quantum mechanics became well known. In this context, the concept of spectrum as a space made of ideals is perfectly analogous of that in operator theory (think of Gelfand-Naimark theory, and that the Gelfand spectrum of the abelian C-star algebra generated by one operator is nothing but the spectrum of that operator).
I wouldn't be surprised if the term "spectral sequence" had something to do with "inspecting" [b.t.w. also "to inspect" comes from in + spècere...] step by step the deep properties of some cohomological constructions.
Maybe the term "spectrum" in homotopy theory and generalized (co)homology -but I don't know almost anything about these- has to do with "probing", "testing", a space via maps from (or to?) certain standard spaces such as the Eilenberg-MacLane spaces or the spheres. Does it sound reasonable?
Edit: The following paragraph from the wikipedia article on "primon gas" seems to support my guess:
"The connections between number theory and quantum field theory can be somewhat further extended into connections between topological field theory and K-theory, where, corresponding to the example above, the spectrum of a ring takes the role of the spectrum of energy eigenvalues, the prime ideals take the role of the prime numbers, the group representations take the role of integers, group characters taking the place the Dirichlet characters, and so on"
Best Answer
After my article was published, John Harper sent me email and said that when he was a graduate student back in the 1960s, he personally asked Leray about the term "spectral" and in particular asked whether it had something to do with the spectrum of an operator. Leray began his reply by saying, "Non"; unfortunately, before he could continue, some professors approached and interrupted the conversation.
This is perhaps some weak evidence that the spectrum of an operator is not what Leray had in mind, but unfortunately gives us no more positive information about what he did have in mind.