This phrase seems to be Silicon Valley slang. Used generally, it refers to believing religiously in the New Economy; more specifically, it's used to refer to believing your own propaganda, or that of whoever you're with: You're on the team, "signed up", committed to the madness at hand, etc.

I'm guessing that it derives from the LSD-spiked Kool-Aid in The Electric Kool-Aid Acid Test by Tom Wolfe.

References:

Sense 1:
    http://www.lvdi.net/~intercon/Archive/SUM0706.TXT

Sense 2:
    http://www.salon.com/tech/feature/1999/10/13/vc_class/index2.html
    http://www.wired.com/wired/archive/8.04/jwthompson_pr.html


I've also heard it used, only once, in the Jim Jones/Heaven's Gate sense of "Kool-Aid": A VC who has "drunk the Kool-Aid" is one who has pumped enough money into your cult that he'll have no choice but to die with you when the time comes. The more I think about it, the more I doubt that this usage differs from the above, except in the sense that the speaker has thought it all through.