Baseball America revealed the bottom half of their top 100. Jeremy Sowers came in at #53 and Brad Snyder checked in at #71. Since Andy Marte (a guess, but pretty sure) and Adam Miller were ranked ahead of Sowers and Snyder in the team's top 10, the Indians will have 4 of the top 100.
John Sickels of Minor League Ball (and author of The Baseball Prospect Book) has released his top 20 Indians prospects. The only real surprise on my part is that Franklin Gutierrez didn't even make the list. He doesn't like Fausto Carmona either. Adam Miller and Michael Aubrey were downgraded because of injuries.
Overall, I think it's fair to characterize the system as having one or two "elite" prospects and a lot of depth. Injuries have hurt, with players like Michael Aubrey, JD Martin, Scott Lewis, and Matt Whitney being shut down with serious to career-threatening injuries in recent years. But even with those injuries and the graduation of several good prospects to the majors, the farm system is still in pretty good shape.