U.S. Box Office: $171 million
Actual nominees that year:  "American Beauty," "The Cider House Rules," "The Green Mile," "The Insider," "The Sixth Sense"
Winner: "American Beauty"

Justification: A tough one.  "The Matrix" was a monster hit, but it's impact wasn't really felt until a few months after its release.  That coincided directly with awards season and while the Wachowski's ground breaking thriller made many ten best lists what was most telling was it's Oscar nomination for best editing.  That's a key branch in the Academy and is enough evidence to safely say there would have been enough support to get it in if there were ten nods that year.  

Other potential nominees: "The Talented Mr. Ripley," "Boys Don't Cry," "Being John Malkovich," "Notting Hill," "The End of the Affair."

[Note: With both directing and screenplay nods, it's a lock to say "Being John Malkovich" would have also made a larger pool.]