Hmm off the top of my head I enjoyed QED (Katou Motohiro), CMB (Katou Motohiro) and the Kindaichi series, the mysteries here are generally standalone though rather than an overarching one like this.
For ones with an overarching mystery, Tantei Gakuen Q (Shin Kibayashi, Satou Fumiya), Migi and...
All I'm getting now is the throwback to Kyoko's school bully role, honestly, iconic. It's been so long since I read this series and also, since I started the series lol