People routinely boot DOS in e.g. qemu. The x86 ISA is 45 years old, older if you consider the 8008/8080 part of the lineage. It's not pretty, but it's probably the most widespread backwards compatible system out there.
S/360 assembly programs probably would still run on a modern IBM mainframe.
Punched cards kept in an inert atmosphere probably would last for centuries, and along with printed documentation in archival-quality paper would allow future generations to come up with card readers and an emulator to actually run the program.
