Franchise Killer: Clock Tower 2: The Struggle Within, aka Clock Tower: Ghost Head, may be what killed the franchise due to faulty game play mechanics, dated graphics, a story that was all over the place, and possessing fake difficulty. Although, Clock Tower 3 made an attempt to revive it, while Haunting Ground (originally a sequel) became a one-off spiritual successor.
No Export for You: The original SNES game, and the updated PC and PlayStation re-releases thereafter.
Word of God: Hifumi Kouno, the director of the first two games, responds to fan e-mail and has answered several questions about the series in his replies. (Most of the questions and answers can be found in this forum topic, but additional ones can be found here and here.)