Over at Royals Review, I compiled all of Baseball America's top 100 prospect lists going back to 1990. Here is a link to a spreadsheet with all the data:
The last page of the spreadsheet contains a complete list for all the years. Some of the data may need to be cleaned up, but I am not in the mood right now. I hope someone else finds it useful and they don't have to go through the bordom of creating it themselves.