The 3D Realms Forums (thanks Voodoo Extreme) offer the news that the Triton digital distribution service is shutting down (or has already done so, as their site is 404 "not found" as of this writing). The service was responsible for the digital distribution and management of Prey, and without it running, download copies of the game cannot authorize and launch. Until things are cleared up further, even 3D Realms is unclear as to what this all means. Here's the post by web-guru Joe Siegler:

After checking into it, we have been informed that the Triton service is shutting down - we should have some information about this situation shortly.

I don't have any further information about how things will all play with with keys, reg codes, Triton, logging in, or anything else at this time.

I'm looking into it - I swear, as soon as I have some more info on all this, I will let you know.