I think Black Org is still kind of interesting, but after Bell Tree express arc, things got rather shallow. I really wish things kind of picked up after what Vermouth told Mrs. Kudo, as that was the perfect moment to start revealing more about them.
Favorite villain of detective fiction, huh? Let's see. I find Moriarty fairly interesting, which is probably why The Final Problem is one still fairly enjoyable to me, and a close second would be Mr. Brown.
There are one or two others that I like, but they more fit under crime fiction than detective fiction.