I was at the University of Maryland Book Center the other day, and in the Bargain Bin was a 1999 Scouting Guide for 3.98, so I thought it was worth the investment.
I checked out Moise Alou, who during this time was on the Astros. 1998 was his best season to that point. An interesting fact about 1998 Alou is that after 0-2 count, his batting average was .000. He also led the Astros in most offensive categories. That year he had 38 homers, and probably would have won the MVP if he hit some homers in September.
In this book Adam Dunn is a Red Minor League Prospect. Vernon Wells was a prospect as well, with Roy Halladay. In the Yankee system, Ricky Ledee, Mike Lowell, Alfonso Soriano and Nick Johnson were all prospects.