Zoinks!!! While they never crossed paths in the comics during Scooby-Doo's brief stint at Archie Comics, the Great Dane and his BFF, Shaggy, meet Sabrina, The Teenage Witch, during the final season of the series.
"Sabrina Unplugged" is not available online in its complete form, so all we have is this brief snippet in which Sabrina (Melissa Joan Hart) literally goes online and meets Scooby (Frank Welker) & Shaggy (Casey Kasem). Sabrina had moved from ABC to WB two years earlier, and What's New Scooby-Doo had launched a few weeks prior to this episode airing.
Chalk it up to the network looking to test the waters of Scooby in primetime before his Christmas special aired two months later.