I guess the problem with the historical value of the lists problems begin with different writers. Baseball America and John Sickels are the only places that have been forming a list for 8+ years with at least the main person making the call on the list. Even BA rotates some writers in and out as far as their Top 100 meetings go, and the team rankings have probably 10-15 different people making the lists, though I believe Callis does have final say there. With that said, Victor Wang has done some research on the value of those two lists rankings. You can see that at The Hardball Times
The problem with that is that the data is based on lists from 1990-1999 and surely things have changed somewhat since then in how evaluators are ranking prospects.