Quite a task indeed! From the sounds of things, you only want a list of cards, not a card collecting database (as the others have suggested). I've got an Excel file that includes the following *American* sets....
Yugi Starter Deck
Kaiba Starter Deck
Joey Starter Deck
Pegasus Starter Deck
Legend of Blue Eyes White Dragon
Metal Raiders
Magic Ruler
Pharaoh's Servant
Labyrinth of Nightmare
Legacy of Darkness
Pharaonic Guardian
Tournament - 1st Season
Tournament - 2nd Season
Tournament - 3rd Season
Limited Edition Booster Pack Tins (1-6)
McDonald's Mighty Kid's Meal #1 (1-15)
Duelist League Cards (1-2)
Game Boy Color - Dark Duel Stories
Game Boy Advance - The Eternal Duelist Soul
Game Boy Advance - Stairway to the Destined Duel
Playstation - Forbidden Memories
Playstation 2 - The Duelists of the Roses
Shonen Jump Magazine (1)
I'm not sure how out of date it is (around 2 years...)but I'm sure with a little work, it could be updated with newer American sets, and possibly even all of the Japanese sets.
**EDIT**
After some poking around, Upper Deck's site has a checklist function on their
product page. From the look of things, the "Find Checklist for" function lists them in *reverse* order of American release. Very easy to copy/paste and import (well..with a little work....)