This is an important question. I read an article (can't find it now) about museums tackling this problem for their digital born art. The idea is to encapsulate the binaries that run the art in some way that is human readable, or at least, in a way where humans could re-engineer the software, so you don't run into issues where in a thousand years there are no more Flash players.
It's a hard problem if you consider long time scales.