I let the character grow organically, molded by his adventuring experiences. I rarely start out a 1st-level character with a prestige class already in mind, unless it's something really obvious like Red Wizard of Thay for a Thayan wizard character, and even then, if campaign events render the choice unviable or present me with a better one, I never hesitate to change my mind.
My current Living Greyhawk character, the wizard Xaylen Ambedor, is a good example of a character who grew during his adventures. Originally, I geared him for survival. His beginning feats were Toughness and Rapid Reload. In the first adventure, the party just set off a trap that dropped the boulder from Raiders of the Lost Ark into the same dead end corridor with them. The DM gave us one round to prepare for the impact. Some guys went on full defense, a few healed themselves and I, with my spells extinguished and lacking in hit points, looked at my character sheet... looked at the battlemap, looked at the DM... and said "I find God."
The boulder rolled a one and missed me. Every other guy in the group was knocked in the negatives.
And now, over a year and seven character levels later, my character has finally got his first level of Divine Oracle of Boccob.
It's lovely when things work out that way. Prestige class prerequisites are pretty much the only thing I'm willing to plan out very far, and even that's just because they're pretty much necessary.