The Book has a nice approach to assembling a lineup. Simply put (details here), you split your 8 starters up three ways - the top 3 hitters, the middle 2 and the rest (AKA The Professor and Mary Ann + 1). You can also estimate the production of a lineup with David Pinto's tool, which 'll use to compare three lineups. Or, really, compare two and let the tool pick a third. Casey Stengel makes a cameo towards the end - stick around!
Here are the inputs, from CHONE.
Building by The Book
The bottom three take care of themselves, rather easily. Fukudome projects mildly positive, Fontenot takes it negative and Theriot goes a baker's dozen under.
I'm not going to go with the pitcher batting 8th, sorry Big Z.
Actually, I'll take that back. Zambrano should hit in the 9th spot, but Harden, for example, would go in the 8th slot. If you check out this thread, you'll get the idea that bad hitters, really bad hitters, should be "isolated" from the better hitters found at the top of the order. And a reminder that egos need to be tended. Flip a coin on Big Z - an ego spot or 9 spot. Even though putting him 9th does mean he's a better hitter than his rotation mates.
Back to the bats at the top ...
The best three hitters should fill the 1,2 and 4 spots. Bradley, Ramirez and Lee are clearly the guys - Lee goes first, since he's the least reliant on home runs, Aramis is the most reliant on the bomb, putting him 4th, leaving Milton, appropriately, with his high OBP:SLG ratio in the second spot. You could justify a switch of Lee and Bradley. If you want Lee to continue to GIDP like crazy.
The Book says to put the best remaining hitter 5th, unless he's basically a home run guy and not much else. It's hard to say, based on CHONE, who the better hitter is, but Soriano fits the home run guy mold better than Soto. So, Fonzie goes third.
Measuring Up to the Alternatives
I ran the lineup in Pinto's tool. Click for full results. The lineup by The Book projects to 5.379 runs per game.
The best line-up, according to Pinto's tool, using CHONE again, yielded 5.614.
This tool-generated lineup flips Lee and Bradley, Fukudome and Soriano, and the pitcher with Theriot. I really think the only significant difference is the flipping of Fukudome and Soriano.
Lou Piniella has told the media a bit about his 2009 lineup already. This likely Cubs lineup projects to 5.317 runs.
Mr. Stengel has a bone to pick. Whether it be my take on the The Book's technique, or Lou's or Pinto's, old Casey might suggest changing some stuff against left-handed starters.
As far as my Book-based creation, I don't think anything would change order-wise. Simply plug in Reed Johnson and Aaron Miles, and possibly re-order the 6-8 spots a little. I don't think anything useful would come of that, so I'd probably leave it alone.
Lou is faced with a bigger challenge - or at least I think so. The 2 and 6 spots will probably get filled by Miles and Johnson, respectively. I would hope Soto gets moved up a spot. Even against righties.
Pinto's tool doesn't let you analyze platoon effects. I'd guess restricting pitchers to lefties would cause a bunch of changes, moving things around more than the other options discussed.
Without regard to the platooning, the production for the three lineups over a full season:
Pinto's Best: 909 runs
The Book: 871
Taking the output of the tool at face value, The Book will beat Lou by one win (assuming they both manage the pitching staff the same, hah) but falls short of Pinto's Best by almost four wins.