I suspect that there are many more, and which papers are important to any one person is as varied as the disciplines we have within software engineering.
- Out of the Tar Pit 2005, a paper on Functional Reactive Programming that is an excellent read for anyone doing functional programming, UI programming, or a number of other things.
- Consistent Hashing and Random Trees: Distributed Caching Protocols for Relieving Hot Spots on the World Wide Web 1997, important read for anyone working in distributed systems or services with any sort of scale.
- Roy Fielding's dissertation 2000, to learn just how widely applicable REST principles are and how misunderstood it is as a design.
- The Part Time Parliament 1998, the original Paxos paper, important basis for anyone working with distributed systems.
- The Cathedral and the Bazaar 1997, an essay not a paper, but a good background to the open source world.