These are only some of the characters who made science cool (and sometimes scary)...
Dana Scully - The FBI agent, played by Gillian Anderson, had a degree in Physics and went to medical school. She was the skeptical foil to her partner Fox Mulder as they investigated paranormal activity on The X-Files.
Victor Frankenstein - Author Mary Shelley practically invented the mad scientist stereotype (and the science fiction genre) with her story Frankenstein or The Modern Prometheus, about a genius who finds a way to create new life from patchwork corpses.
Emmett Brown - Christopher Lloyd's depiction of this frazzled inventor who creates a time-travelling car was one of the highlights of the excellent Back to the Future trilogy.
Henry Jekyll - Writer Robert Louis Stevenson tells a gripping tale in his novella The Strange Case of Dr. Jekyll and Mr. Hyde, in which a well-meaning scientist's experiments on himself release the dark side of human nature.
Spock - Star Trek had some great characters, including Medical Officer Dr. McCoy, but one of the most popular was the pointy-eared Vulcan, Mr. Spock, the U.S.S. Enterprise's second-in-command and cool as a cucumber Science Officer, played by Leonard Nimoy.
Paul Moreau - The title character and primary antagonist in the novel The Island of Dr. Moreau by H.G. Wells had no first name, but the movie versions dubbed him Paul. Played by Burt Lancaster, Marlon Brando, and others, the character's biology experiments (and later genetic engineering) resulted in human-animal hybrid monstrosities.
Walter Bishop - One of many great elements of the TV show Fringe is the portrayal of the complex character Dr. Bishop by actor John Noble. He's quirky, he's funny, he's emotionally damaged, he's brilliant.
Jack Griffin - H.G. Wells gives us another mad scientist type in his novel The Invisible Man, in which a scientist discovers the secret of invisibility only to spiral more and more down the path of corruption.
Sheldon Cooper - The Big Bang Theory is a sitcom about a bunch of friends who happen to be geeky scientists, and Sheldon, played by the award-winning Jim Parsons, is the greatest and funniest of them all.
Seth Brundle - Jeff Goldblum gave an excellent performance in the remake of The Fly, about a scientist whose teleportion device leads to a lab accident in which his DNA and the DNA of an unassuming housefly mix to horrific effect.
Roy Hinkley - Better known as simply "The Professor," Gilligan's Island genius could turn coconut shells, bamboo stalks, fish bones, and palm branches into electrical generators, hot tubs, and other modern luxuries, but he sadly could not figure out how to fixed the damaged U.S.S. Minnow that stranded him and his castaways for years on a tiny island. Actor Russell Johnson played him to dry perfection.
Rudy Wells - Martin E. Brooks portrayed the inventor of bionic technology who created both The Six Million Dollar Man and The Bionic Woman.
Dan Henderson - If you have children, you should watch the kids' show Dino Dan, in which a young boy (played by Jason Spevack) uses the scientific method, and his wild imagination, to learn everything there is to know about dinosaurs.
The scientists of C.S.I. - The lead characters from the Crime Scene Investigation franchise use their science skills to solve heinous murders. It all started with William Petersen as Dr. Gil Grissom in Las Vegas, followed by Lt. Horatio Caine (David Caruso) in Miami, Detective Mac Taylor (Gary Sinise) in New York, and Dr. Raymond Langston (Laurence Fishburne) replacing Grissom in Vegas.
I've left out a bunch. Let me know your favorites.