I would never call it my "all-time favorite" (no paper qualifies for that title in my book), but Satoshi Nakamoto's paper, "Bitcoin: A Peer-to-Peer Electronic Cash System" deserves a mention here, because it proposed the first-known solution to the double-spending problem in a masterless peer-to-peer network, with Byzantine fault tolerance (i.e., in a manner resistant to fraudulent nodes attempting to game the rules), via a clever application of proof-of-work:

https://bitcoin.org/bitcoin.pdf

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 :-)