IMO, CP9 in Water 7 > Baroque Works >>>> CP9 in Enies Lobby
CP9 in Water 7 was downright terrifying. Not only did they seem absolutely unbeatable, but the added twist of them posing as allies just made them more compelling -- especially since it was the OG 4 of Lucci, Kaku, Kalifa and Blueno.
By EL, Oda added a few clowns for volume and gave them comparatively goofy designs/abilities and worse skills, essentially just tanking their villain-ness. Spandam obviously didn't help either lmfao.
Baroque Works has a very good mix of interesting personalities, perceived threat level, and far-reaching story relevance. Not to mention that the entire crew was pretty damn fucked up after that battle. The Straw Hat victories from those fights are a lot more memorable in my opinion.
Though lowkey I would argue that Enel and his priests are the scariest antagonist group in the story lmfao.