Kirk on the Enterprise vs. Khan on the Reliant, in "Star Trek II: The Wrath of Khan."

Right behind it, though, are Kirk & Co. vs. the cloaked Romulan ship in "Balance of Terror"; and Enterprise vs. the Klingon ship at the climax of the otherwise terrible story "Elaan of Troyius."

Oh, and Enterprise vs. "The Doomsday Machine." ("I shall be forced to relieve you [on the grounds you are insane], Commodore." "You're bluffing." "Vulcans never bluff." And after a measuring glance at Spock: "No. No, I don't suppose that they do. . . .")

However, if we're talking outside movies/TV, the climax of Larry Niven & Jerry Pournelle's alien-invasion novel Footfall stands as the champ.
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-- Paul W. (The Benzadmiral)
('03 Buick Park Avenue, charcoal/cream)
Formerly:
'97 C230, smoke silver/parchment; '86 420SEL, anthracite/light grey; '84 280CE (W123), dark blue/palomino