Human v Chimp - How different?

From House, M.D. -
Dr. Foreman: "Her oxygen saturation is normal."
Dr. House: "It's off by one percentage point."
Foreman: "It's within range. It's normal."
House: "If her DNA was off by one percentage point, she'd be a dolphin."

We're not that close to dolphins, but we've heard interminably that humans and chimps share 98% (give or take 1%) of our DNA with chimps. Well, then why are we different in many obvious ways? According to researchers at Georgia Tech, that nearly-identical genome is significantly affected by gaps (not physical gaps, but areas filled by "junk" sequences called retrotransposons) surrounding the genes and determining which genes are expressed (turned on) and which are not. That raises some interesting mad-scientist experimentation ideas for the writers of Crichton-type fiction.