What is the vertical complement of side-by-side?

In the context of design - especially website design in my experience - one would say "Beryl Green" and "Albescent White" were stacked vertically.

Yes, see, http://www.cabelas.com/category/Over-Under-Side-by-Side-Shotguns/104802480.uts

Double-barreled handguns, notably Derringers are also produced in an over-under configuration. Google "under-over Derringer" and choose "Images", and you'll see many examples.

Apart from firearms, you could use the word "adjacent". Miriam-Webster's Thesaurus also suggests, "abutting, adjoining, bordering, conterminous, contiguous, flanking, flush, fringing, joining, juxtaposed, neighboring, skirting, touching, verging". My own experience is that for the two colored boxes the more commonly-used words of those listed would be "adjacent", "abutting" and "adjoining", in that order. Since so many disparate objects may be side-by-side, a generic use-frequency survey, like Google's, would not be very persuasive. For example, if you had presented a photo of two houses, the most common joint adjective would likely be "neighboring".