They were never totally secret.
The "Total Information Awareness" program, or as it was later known, "Terrorism Information Awareness" program was supposedly killed by Congress when Congress cut off funding due to concerns about the extensive data-mining capabilities (and consequent civil liberty implications of misuse of same) envisioned by DARPA, under whose auspices the program was to be developed.
TIA intent, DARPA said, was to "protect citizens by detecting and defeating foreign terrorist threats before an attack." Sounds a bit like the language Bush used when describing the NSA surveillance program the other day, doesn't it? Hence, the suspicion in some circles
that some aspect of TIA has lived on or been resurrected for the current surveillance program.
The Electronic Frontier Foundation continues to maintain info on its website, here