Updated 4/3: Added Blue Jays.
Updated 3/29: Added Tigers, Diamondbacks, Rockies, and another Mets analysis. Also, PECOTA projects L/R splits for AVG/OBP/SLG, which is really the way to go. You have to search player by player, though.
I'm quite excited with how many blogs ran with the idea of optimizing lineups by The Book. (My original article is here.) Rather than continue to post a FanShot on the front page every time another one pops up, I'm going to add links to this thread, which I'll mark as a Featured Story (meaning you can find a link to it in the right sidebar on the front page) and bump as new articles are added. I know I've seen more articles than what I've linked to below, so let me know what I've missed up to this point...
National League
Mets (MG) | Phillies | Marlins | Nationals | Braves
Cubs | Cardinals | Reds | Astros | Pirates | Brewers
Giants | Rockies | Dodgers | Diamondbacks | Padres
American League
Yankees | Red Sox | Rays | Orioles | Blue Jays