Others in this thread have already mentioned papers or opinionated essays that quickly came to mind, including "Reflections on Trusting Trust" by Ken Thompson, "A Mathematical Theory of Communication" by Claude Shannon (incredibly well-written and easy-to-follow given the subject matter), and "Recursive Functions of Symbolic Expressions and Their Computation by Machine" by John McCarthy.
I would also mention "On Computable Numbers, with an Application to the Entscheidungsproblem" by Alan Turing, "On Formally Undecidable Propositions of Principia Mathematica And Related Systems" by Kurt Gödel, and "The Complexity of Theorem Proving Procedures" by Stephen Cook, but in my view these papers are 'unnecessarily' challenging or time-consuming to read, to the point that I think it's better to read textbooks (or popular works like "Gödel, Escher, and Bach" by Douglas Hofstadter) covering the same topics instead of the original papers. Still, these papers are foundational.
Finally, I think "The Mythical Man-Month" by Fred Brooks, and "Worse is Better" by Richard Gabriel merit inclusion here, given their influence.
This is by no means an exhaustive list. Many -- many -- other worthy papers will surely come to mind over the course of the day that I won't have a chance to mention here.
There are many other good recommendations elsewhere in this thread, including papers/essays I have not yet read :-)
Fyi, the original paper by Ralph Merkle where he introduces what is later called Merkle Trees is definitely worth knowing. I wouldn't say it is my fav, but it resulted in a key component in some of my favorite technologies.
An amazing contrast: "Publish or perish" driven research vs "I don't want the fame, I just want to build something useful and practical".