Ooh, great question! I would say "A Gaggle of Galloping Ghosts," just because it utilizes the classic horror movie film monsters. I also love it for nostalgia purposes, since this was the first Scooby episode I ever saw as a kid!
Both episodes also feature a male bad guy crossdressing as part of his spooky disguise. The difference was though, with "A Gaggle of Galloping Ghost," Big Bob Oakley was voiced by John Stephenson, but when he was disgusied as the gypsy fortuneteller, June Foray did his fake woman voice (TVTropes calls that "Cast as a Mask.") But with "Which Witch is Which," the Witch's voice was done by Don Messick. And even though we didn't hear Zeb's real voice, it's same to assume Don Messick would've done his real voice as well. (Yes, when I rewatched the episode a while back, I could hear Don Messick in the Witch's voice, as it didn't sound like a real woman doing the voice, like when Jean Vander Pyl would voice Winsome Witch on "The Secret Squirrel Show.") I have to say that was a pretty realistic touch there, having Don Messick imitate a witch voice for Zeb disguised as the Witch.