I take a look at the characters and try to emphasize their strengths in play.
For instance, my last group's only rogue was multiclassed, which meant she didn't have many points into Disable Device. So I minimized traps in our games.
My next group likely will have no cleric, so I'll minimize undead and change turn undead in order to use the Complete Divine option, which allows the paladin to be effective and the party will be able to pitch in.
I ran the Adventure Path. In FoF, the PCs are hired by a noble to retrieve masterwork weapons. Knowing that I'd run SiD, I changed the noble in FoF to be the baron from SiD, instead of just throwing in a random noble.