If you haven’t played it yet, The Wolf Among Us has elements of a good whodunit and is overall a good game - but not a great one. More importantly, I think it might give some good pointers in how to fill the space between the puzzle pieces, so your story doesn’t look like a straight-up tunnel and it shows off some pitfalls that you can then avoid in your own game. ;) And for that reason, I would recommend The Wolf Among Us to you.
I thought I had played more of these games, but on closer inspection, most of the ones I had thought of don’t really fit the specification… I can give you “a” list of detective-y games, but I wouldn’t think trying to emulate The Infectious Madness of Doctor Dekker[*] or Her Story would be what you’re after.
On top of that my current issue is that I am interested in a lot of games, but I can’t make the time to actually play them. The (aforementioned) Tex Murphy series and The Dame Was Loaded seem good, but I couldn’t personally vouch for them actually being good or standing the test of time. (I bought the Tex Murphy series and looked into buying The Dame Was Loaded, if that’s any help…)
[*] Truth be told, I wouldn’t describe The Infectious Madness of Doctor Dekker as “enjoyable”, due to the topic, but it was… interesting. Not so interesting to inspire a second playthrough though…