Baseball America: Jim Callis, John Manuel & Co. have been the premier source for prospects the past two decades. The Daily Prospect Report is highly recommend. Every day, it sends an email with the statistics of about 100 top prospects.
Baseball De Cuba: Information about Cuban baseball is difficult to find, but these guys do a good job. My favorite part of the site is, during the season, they provide a link to a place where you can view webcasts of National Series games.
Baseball-Reference: The most comprehensive source of baseball statistics online.
Bullpen Banter: Interesting prospect-related analysis on a site started by several frequent posters on Minor League Ball.
Crawfish Boxes: The site I visit daily to learn about the Astros. David Coleman is a good writer, and the site has made life easier from struggling ‘stros fans.
ESPN: Keith Law is ESPN’s resident prospect-follower. His chats and comment responses are always entertaining, and lately, he does a blog with Jason Churchill leading up to the major league draft which is a good read. Needless to say, the baseball content from Buster Olney and Jason Gray is awesome too. The weak spot is a lot of the content requires Insider.
Fangraphs: Fangraphs does an incredible job making advanced statistics more accessible, and every day, there are multiple articles containing interesting statistical discussions.
Fantasy Rundown: A terrific source of fantasy baseball information that compiles various news and a terrific compilation prospect lists.
First Inning: The “Your Page” section has provided a much-needed way for people to efficiently track the day-to-day progress of particular players (prospects and major leaguers).
Hardball Times: In addition to the current content, you can learn lots by reading the archived materials on this site. For example, Victor Wang wrote some incredibly interesting stuff a few years ago about analyzing prospects.
Joe’s Baseball Blog: A blog started by one of Deep Leagues’ first commenters…contains prospect lists and some solid baseball analysis.
Minor League Ball: John Sickels’ SB Nation site is becoming one of the fastest-growing prospect-related sites. In addition to John’s writings, there is always an interesting discussion in the “fanposts” section.
Milb.com: Even though it costs money, MILB TV is a worthwhile purchase for people who want to watch prospects in action. Also, the site itself has greatly improved and going through the box scores has been much less of a hassle.
MILB Insider: After spending years focusing on football/basketball recruiting, the scout.com network is finally getting into baseball prospects. They hired Frankie Piliere (whose stuff on AOL was really good), and this site could become a great source of prospect coverage.
Minor League Splits: Unfortunately no longer active, but in recent years, the spreadsheet from minor league splits (while it takes some time to learn to use it) was a great place to obtain statistical information about prospects which was not available elsewhere.
Project Prospect: A solid prospect site which always contains interesting analysis.
Rob Neyer: Neyer recently switched from ESPN over to SB Nation. He has been one of my favorite writers for years, and always provides interesting information.
Rotoworld Forums: one of the most active baseball-related message boards.