Season 1

Book 1
Swing Shift: Director’s Cut
Amazing Spider-Man 546 (backups)
ASM 546-567
ASM Extra 3 (story 3)
ASM Extra 1

Book 2
ASM 568-574
Secret Invasion: ASM 1-3
ASM Annual 1 (35)
ASM 575-582
ASM Extra 2
ASM 583-588
ASM Extra 3 (stories 1-2 and sketches)

Season 2

Book 1
ASM 589-599
Dark Reign: Mr. Negative 1-3
ASM Annual 36
ASM 600 (main story and last story)
ASM 601-610
Peter Parker 1-4
ASM 611
Amazing Spider-Man 600 (backup features)
ASM Gauntlet Sketchbook

Book 2 – The Gauntlet
ASM 612-629
ASM 628 (backup)
American Son 1 (backup)
ASM 629 (backup)
ASM 630-633
Web of Spider-Man #7 (first story)
Grim Hunt: The Kraven Saga (main story)
ASM 634-637
ASM #634-637 (backups)
Grim Hunt: The Kraven Saga (back up features)

Book 3
Web of Spider-Man 8-10
Peter Parker 5
Web of Spider-Man 9-11 (backups)
American Son 1-4
Amazing Spider-Man 638-641
Web of Spider-Man 11-12
ASM 642-647
Spidey Sunday Spectacular

I opted against using the first half of the Web of Spider-Man series, and also dropped a lot of the extras that would go into a companion book. I also included the backup story from #601, leaving it in place. It probably should go into New Avengers, but then we would lose the letters page here, and it would be tricky to force it into the middle of that stretch of New Avengers.