While I think the Cell Saga is probably the most entertaining overall, I happen to think Frieza is actually the best villain. Frieza had the most build up, and the highest emotional significance to the characters. His ambition was the most practical, which made his evil actions the most understandable. Not only was he incredibly powerful and seemingly undefeatable, his flaws also made him interesting. His fear of Saiyans was deeply ingrained which made his superiority complex highly unstable. He wanted to believe he was the strongest, but deep down he feared he might not be. It's his doubt that made him such an interesting character.