Here are some stories I found good besides the stories you and others have mentioned.
Spider-Man Blue great story that really gives a lot to Peter's lost of Gwen Stacy.
The Death of Jean DeWolf - One of the best team up stories with Daredevil. Sadly OMD has erased the ending however still a good story.
Spider-man 2099 - Peter Davids take on spider man set in the future. A very interesting concept and with Peter David (know for his long Hulk run) as writer it is a no brainer. It is not PP that are sent to the future but about Miguel O'Hara that are very different from PP. There has been released two tpb's so far the first one is definitely the best.
Cult of Love - Sadly not collected in a trade. Another story by Peter David the story shows the relationship between PP and Betty Brant and his feelings. It is probably not very important for the modern day understanding of PP but a nice corner to visit.
JMS* Spider-man run - It is different since it takes a more spiritual look at Spider-man but it is still very very good.
Torment - Todd Mcfarlane both as a writer and penciler probably the scariest Spider-man story ever told.
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