My favorite moment would be when Tony locked him in the secret room in 1985 (their final scene together for years; Sindacco posted it above). Such great acting.
I think the most iconic scene, however, has to be Stefano shooting Roman and Roman's subsequent fall off of the cliff in 1984. It's probably his most famous scene (in fact the most famous scene of any daytime villain), and it changed the course of Days' storytelling history in ways that are still felt today nearly 30 years later.
seconding this post
and adding the clip with the Roman/Stefano scene (begins at 2:07)
That's what seperates Stefano from Tony and EJ. He wasn't willing to rape the woman he claimed to love.
Tony wasn't in love with Liz when he raped her. He was in love with Renee.