Apparently, 80 players were named as having used steroids, HGH, and other "performance-enhancing drugs" (if there are any others that are not steroids or HGH, that is). The most notable of those names are 7-time Cy Young winner Roger Clemens, his teammate on two teams since 1999, Andy Pettitte, Miguel Tejeda (who the Baltimore Orioles traded to the Houston Rockets JUST YESTERDAY), Eric Gagne, and of course, Barry Bonds.
The report can be found here, but be warned; it's 409 pages.
There was one considerable roadblock in this investigation, though; the fact that the MLBPA (Baseball's players union, in layman's terms) have urged ALL active players to not cooperate with former Senator and leader of the investigation George Mitchell. Most of the leads came from the BALCO investigation, the Kirk Radomski investigation, and the recent investigation conducted by the Albany, NY District Attorney's office.