Don't forget the freebies from Green Ronin's site!
http://www.greenronin.com/freeportfocus.shtml
The Consequence of Vice: This Freeport adventure by William Simoni originally appeared in the ENWorld Player's Journal, and is presented here courtesy of our friends at Goodman Games.
Deus Ex Machina: Jeff Quick has cooked up a three-part d20 System Freeport adventure for four 5th to 6th level adventurers.
Holiday in the Sun: Celebrate Freeport's favorite holiday, Swagfest, in this month's Focus on Freeport. Holiday in the Sun is an adventure for character levels 2-4.
Consequences of Vice is about busting up a drug den. It's a major component of my current campaign. I combined the drug den in Consequences of Vice with the drug den in Black Sails Over Freeport, and the two complemented each other nicely.
Deus Ex Machina is silly. I rewrote it significantly for my game.
Holiday in the Sun is a blast and worth playing after the trilogy just so the PCs can engage in the contests. You can read about it in my Story Hour:
http://www.enworld.org/showthread.php?t=103252&page=6
Vengeance in Freeport takes place like a week after the trilogy, if I remember correctly. We played through this one too, but I tweaked it significantly and changed the bad guys around. Nothing quite like having terrorists in Freeport!