I really enjoy reading all the interpretations of the flash :) That said, I may as well lay down the actual storyline (at least once). This seems like just as good a place as any:
In the future, mankind is nearing it's end (nuclear holocaust, global disease, it's unsaid). In order to preserve the legacy of man, our combined knowledge, history, and experience, scientists attempt to create an organic tool capable of surviving the post-apocalyptic world.
This storyline takes place in research area B. Their subject, was the StrawberryClock. What other experiments took place in areas A, C-X ... remain a mystery. The SBC we see (the protagonist) is actually the result of thousands of attempts to create an artificial life-form to serve as the capsule for all mankind's knowledge and experience. Something that could be seen as a type of "madness".
SBC awakens to a deserted research facility. The place is a wreck, and the cause is unknown. He passes the operating room, learning center, cloning farm, discard pile (mass grave), security checkpoint, and makes his way out into the world, which is also in shambles.
The implication at the end, is that SBC not only is the sole surviver of civilization's collapse ... but possibly has the ability to infect other objects ... creating other clocks. Thus beginning a new era ... of clocks.