I tend to prefer more personal stories, since those are the ones that really set Spider-Man apart from other superheroes.

Kraven's Last Hunt is an all-time great: https://www.amazon.com/Spider-Man-Kravens-Last-Hunt-Premiere-ebook/dp/B00PSN2GGK/

Parallel Lives is a classic: https://www.amazon.com/Amazing-Spider-Man-Parallel-Lives-1-ebook/dp/B00ZMZIO92/

To Have and to Hold is one of my favorites: https://www.amazon.com/Sensational-Spider-Man-2006-2007-Annual-1-ebook/dp/B01BE1WEUC/