FanGraphs - In my opinion, the best baseball site around. The data on the site is tremendous, as it includes traditional and advanced statistics for every player and team. Despite the mountains of data, it remains laid out extremely well, as I have rarely struggled to find what I'm looking for. On top of that, FanGraphs has a number of top-notch contributors that churn out several interesting baseball posts every day. The data alone on FanGraphs would make it a go-to site, and the blog alone would make it a go-to site as well. Put them together, and it is THE baseball site.
Mike Curto's Blog - The play-by-play man for the Tacoma Rainiers also does a commendable job of covering the team. Furthermore, his blog posts often contain links to several interesting stories.
MLB Trade Rumors - The best place to look for rumors, trades, promotions, demotions, and transactions in general for all of baseball. The site doesn't feature inside scoops really, but rather collects bits and pieces from all sorts of sources. If you have a Twitter account, they tweet throughout the day with tidbits about things happening in baseball.
FanGraphs Sabermetrics Library - This page is within the FanGraphs website, but it deserves a separate link. Sabermetric numbers don't have to be unapproachable. If a number pops up on this site, or around the internet, and it doesn't make sense, odds are this library can make sense of it.
Minor League Baseball - The official site of Minor League Baseball is the best source for Minor League Baseball. The statistics have steadily expanded each year, and box scores for minor league games are readily available. The site also does an impressive job of organize the overwhelming amount of minor league data. You can search for teams by league, level, and MLB affiliation. I also think the front page does a nice job of mixing in stories about top prospects, random players having great years, and oddities that make Minor League Baseball what it is.
Baseball-Reference - Still the easiest baseball site to get lost on for hours. The historical data available is amazing, and it lends itself way too nicely to clicking on link after link after link. I am especially fond of the Hall of Fame likelihood formulas, as well as similarity scores.
Cot's Baseball Contracts - This site is completely dedicated to current baseball contracts. It is updated constantly, detailed, and accurate. It also lists probably upcoming free agent classes, and offers downloadable spreadsheets with information on on long-term salary commitments for every team.
Cool Standings - This site simulates the remaining games in the season every day, and generate playoff odds for each team based on them. It's a fun, intuitive, and informative way to look at the MLB standings.
D1Baseball.com - With over 300 college baseball programs in Division I alone, looking at all those places for college prospects is incredibly tedious. D1Baseball puts team sites, conference sites, standings, and even summer league sites right at your fingertips.
College Splits - This site has data for every player in Division I college baseball, including park adjusted and competition adjusted numbers. The statistics are wonderful, especially because it is easy for this data to be fragmented all over the internet with the way college sports works. The only drawback is that you need specific names to navigate around the data. It only becomes powerful once you have specific players in mind.