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Jodi BirkholmA Lou Gehrig card in the wallet of the dead explorer in "The Goonies". Actually, it looked like a 1970's Topps issue.
1960 Topps Ted Klu (among many others) featured in "Rain Man".
1955 Topps Rube Walker, 1955 Bowman Duke Snider and 3 1974 Topps Steve Garveys featured in "Mask".
Not the movies, but Marg Helgenberger found a stack of 1974 Topps cards in childhood the dresser drawer of Grissom's nemesis Paul Mullander in an episode of CSI.
A 1968 Topps Yaz was shown in an episode of "The Wonder Years".
A supposed Joe DiMaggio rookie card and a 1973 "mutton chop" Yaz have been featured on "The Simpsons".
A Tony Micelli baseball card was found among Tony's father in law's personal effects in an episode of "Who's the Boss?". Also, one episode revolved around Tony being forced to sell a 1962 Mets autographed ball that his father obtained in-person as a kid because Samantha needed a dress for the prom (or something equally ridiculous).
Might remember more later.