Here is what I would suggest in publication order:
(some have of course, already been mentionned above)
The Very Best of Spider-Man tpb
- Amazin Fantasy #15 - first Siper-Man appearance
- If this be my destiny... The Final Chapter - Amazing Spider-Man #33
- Spider-Man no more - Amazing Spider-Man #50
- The Kid Who Collects Spiderman - Amazing Spider-Man #248
- Whatever Happened to Crusher Hogan? - Amazing Spider-Man #271
- The Sand and the Fury - Amazing Spider-Man #317
- Fathers and Sins - Amazing Spider-Man #365
- The Osborn Legacy - Spectacular Spider-Man #189
Spider-Man: Wizard Masterpiece Edition tpb
- Nothing Stops the Juggernaut - Amazing Spider-Man #229-230
- Hyde in Plain Sight (aka Hyde & Seek) - Amazing Spider-Man #231-232
- The Kid Who Collects Spider-Man - Amazing Spider-Man #248
- Venom Strikes Back - Amazing Spider-Man #315-317
- The Death of Jean DeWolff - Spectacular Spider-Man #107-110
Saga of the Sandman tpb
- The End of Spider-Man! - Amazing Spider-Man #18-19
- Where Stalks the Sandman? - Fantastic Four #61
- ...Sincerely, the Sandman - The Incredible Hulk #138
- Have Yourself a Sandman Little Christmas! - Marvel Team-Up #1
- Time Runs Like Sand - Marvel Two-In-One #86
- Sand Blasted - Untold Tales of Spider-Man #3
Death of the Stacys tpb
- Spider-Man vs. Dr. Octopus/And Death shall come - Amazing Spider-Man #88-92
- The Night Gwen Stacy Died - Amazing Spider-Man #121-122
The Original Clone Saga tpb
- The Delusion Conspiracy! - Amazing Spider-Man #139-151
- Beware the path of the Monster! - Giant-Size Spider-Man #5
- Till Death Do Us Part! - The Spectacular Spider-Man #25-31
- What about Carrion ? - The Spectacular Spider-Man #149
- The Carrion Cure - The Spectacular Spider-Man #162-163
- The Evolution War - The Spectacular Spider-Man annual #8
Origin of the Hobgoblin tpb
- Pretty Poison - The Spectacular Spider-Man #43
- A Night on the Prowl/Double Defeat - The Spectacular Spider-Man #47-48
- In the Shadow of Evil Past/Now Strikes the Hobgoblin - Amazing Spider-Man #238-239
- Ordeals/Sacrefice Play - Amazing Spider-Man #244-245
- The Hatred of the Hobgoblin - The Spectacular Spider-Man #85
- Secrets/Confessions/Endings - Amazing Spider-Man #249-251
Kraven's Last Hunt Epic Collection
- Man Of The Year - The Amazing Spider-Man Annual #20
- High Tide - Spider-Man versus Wolverin - prequel to The Hobgoblin Revealed
- The Hobgoblin Revealed! - The Amazing Spider-Man #289
- Mask - Web of Spider-Man #29 - sequel to The Hobgoblini Revealed
- The Wedges of Sin - Web of Spider-Man #30 - sequel to The Hobgoblini Revealed
- The Big Question - The Amazing Spider-Man #290 - prequel to The Wedding
- Dark Journey - The Amazing Spider-Man #291 - prequel to The Wedding
- Growing Pains - The Amazing Spider-Man #292 - prequel to The Wedding
- The Wedding - The Amazing Spider-Man Annual #21
- The Honeymoon - The Spectacular Spider-Man Annual #7 - Sadly not collected
- Part 1: The Coffing - Web of Spider-Man #31
- Part 2: Crawling - Amazing Spider-Man #293
- Part 3: Descent - Peter Parker, The Spectacular Spider-Man #131
- Part 4: Resurrection - Web of Spider-Man #32
- Part 5: Thunder - Amazing Spider-Man #294
- Part 6: Ascending - Peter Parker, The Spectacular Spider-Man #132
- The Wedding of the Year - Marvel Age #54 - includes interviews, the Shea Stadium and the Newspaper Strip weddings
Birth of Venom tpb
- Invasion! - Marvel Super Heroes Secret Wars #8
- The New Spider-Man - Amazing Spider-Man #252-259
- Chance - Amazing Spider-Man #298-300
- Return of Venom - Amazing Spider-Man #315-317
- Monster Mash - Fantastic Four #274
- Til Death Do Us Part! - Web of Spider-Man #1
Spider-Man vs. Green Goblin tpb
- The Return of the Green Goblin - Amazing Spider-Man #17
- Green Goblin Reborn! - Amazing Spider-Man #96-98
- The Night Gwen Stacy Died - Amazing Spider-Man #121-122
- Best of Enemies - Spectacular Spider-Man #200
Return of The Sinister Six tpb
- Spider-Man: Spirit of the Earth - One shot
- Return of the Sinister Six - Amazing Spider-Man #334-350
Blue tpb
- Spider-Man: Blue - Spider-Man Blue #1-5
Civil War
- Road to Civil War - The Amazing Spider-Man #529-531 + Fantastic Four #536-537 + New Avengers: Illuminate
- Civil War by Mark Millar - Civil War #1-7
Brand New Day
- Brand New Day vol.1 - Free Comic Book Day 2007 + Amazing Spider-Man #546-564 + Spider-Man: Swing Shift
- Brand New Day vol.2 - Amazing Spider-Man #565-577 + Annual #1 + Secret Invasion: The Amazing Spider-Man #1-3
- Brand New Day vol.3 - Amazing Spider-Man #578-591 + Spider-Man: Presidents' Day Special + Spider-Man: Fear Itself + Amazing Spider-Man: Extra #1-3
The Gauntlet and Grim Hunt
Prequels
- Died in Your Arms Tonight - The Amazing Spider-Man #600-601, annual 36 + Amazing Spider-Familly #7
- Red-Headed Stranger - The Amazing Spider-Man #602-605
- Return of the Black Cat - The Amazing Spider-Man #606-611 + Web of Spider-Man #1
The Gauntlet
- Book 1 - Electro & Sandman - The Amazing Spider-Man #612-616, Dark Reign: The List - Amazing Spider-Man + Web of Spider-Man #2 Electro + Sandman origins
- Book 2 - Rhino & Mysterio - The Amazing Spider-Man #617-621 and Web of Spider-Man (vol. 2) #3-4 Rhino and Mysterio origins
- Book 3 - Vulture & Morbius - The Amazing Spider-Man #622-625 + Web of Spider-Man #5-6 origins of Vulture and Morbius
- Book 4 - Juggernaut - The Amazing Spider-Man #626-629 + #229-230 (the original "Nothing Can Stop the Juggernaut)
- Book 5 - The Lizard - The Amazing Spider-Man #630-633 + Web of Spider-Man #6
Sequel
- Grim Hunt - The Amazing Spider-Man #634-637 + Web of Spider-Man #7 + Grim Hunt Prologue + Spider-Man Origin Of The Hunter
More Sequels
- Origin of the Species - The Amazing Spider-Man #642-647
- Kraven's First Hunt - The Amazing Spider-Man #663-667
Big Time
- Big Time - Amazing Spider-Man #648-651
- Spider Island - Amazing Spider-Man #659-660, 662-665, 666-673 + Venom (2011) #6-8 + Spider-Island: Deadly Foes + Spider-Island Spotlight
- Ends of Earth - Amazing Spider-Man Ends of the Earth #1 + Amazing Spider-Man #682-687 + Avenging Spider-Man #8
- Dying Wish - Amazing Spider-Man #698-700 + Amazing Spider-Man #699.1 + Avenging Spider-Man #15.1
Superior Spider-Man
- Superior Spider-Man Vol. 1 - #1-5 + Amazing Spider-Man #698-700
- Superior Spider-Man Vol. 2 - #6-16
- Superior Spider-Man Vol. 3 - #17-31
Spider-Verse
- Amazing Spider-Man #7-15
- Superior Spider-Man #32-33
- Spider-Verse #1-2 + Spider-Verse Team-Up #1-3
- Scarlet Spiders #1-3
- Spider-Woman #1-4
- Spider-Man 2099 #6-8
- Free Comic Book Day 2014
Ultimate Spider-Man: Death of Spider-Man
- Death of Spider-Man - Ultimate Spider-Man #156-160
Back in Black
- Back in Black - Amazing Spider-Man #539-543 + Friendly Neighborhood Spider-Man #17-23, Annual #1
All-New Ultimate Spider-Man: Miles Morales
- Miles Morales: The Ultimate Spider-Man Ultimate Collection Book One - Ultimate Fallout #4 + Ultimate Spider-Man vol.2 #1-12 + Spider-Men #1-5
- Miles Morales: The Ultimate Spider-Man Ultimate Collection Book Two - Ultimate Spider-Man vol.2 #13-28, 16.1
- Miles Morales: The Ultimate Spider-Man Ultimate Collection Book Three - Cataclysme: Ultimate Comics Spider-MAn #1-3 + Ultimate Spider-Man vol.2 #200 + Miles Morales: The Ultimate Spider-Man #1-12
Secret War
- Secret Wars - Free Comics Book Day 2015: Secret Wars #0 + Secret Wars #1-8
Renew Your Vows
- Amazing Spider-Man: Renew Your Vows - Amazing Spider-Man: Renew Your Vows #1-5, Secret Wars: Secret Love #1