There are a handful of Spider-Man stories that I have several copies of, and I wonder if you guys have similar stories.
I have plenty of Stern's Spider-Man stories in three formats.
For a long time, the Roger Stern Hobgoblin stories were a major hole in my collection. Then I got an out of print copy of the Origin of the Hobgoblin TPB. A few years later, I got a newer version of that TPB.
I also have several copies of the first year of Stern's Spectacular Spider-Man run thanks to the Essential Spectacular Spider-Man TPB, and the Masterworks TPB.
I have Stern's Black Cat story in Spider-Man Megazine #2, and the Spider-Man VS Black Cat TPB.
And then I got the Stern omnibus, which meant that I have three ways to read all of the above.
The Harry Osborn on drugs storyline is part of my favorite Spider-Man TPB Spider-Man VS The Green Goblin. It was later collected in Essential Spider-Man Volume 5. Then it was included in the Marvel Visionaries: Stan Lee hardcover. So I also have three copies of it.
Since I also own the Amazing Spider-Man DVD rom with scanned copies of the first 500 issues of ASM, I have many of these stories in four formats.