The President now admits that there were indeed secret CIA prisons and secret CIA rendition flights.
http://news.bbc.co.uk/1/hi/world/americas/5321606.stm
http://voanews.com/english/2006-09-06-voa47.cfm
I recall OT members strenously denying that such things existed.
The takeaway, to me, is that whatever secret thing the government is alleged to be doing, you may assume they are indeed doing it unless a high-ranking government official (a Cabinet officer or higher, not some sacrificial flunky) is placed under oath and unambigiously denies it under penalty of perjury.
I don't personally have a strong feeling about whether CIA prisons are a good or bad thing, but I think they should operate with some degree of oversight.