Disclaimer, I work for a large contemporary art museum in New Media. We deal with this stuff all of the time and it's something I have an interest in (obviously). The answer for you is there is no tried and true method for archiving digital media. Every arts institution struggles with this, especially when it relates to computational or internet enabled or social media works of art. There are various opinions on what it even *means* to archive some of this stuff and there are varying degrees of opinions out there about all of it.
That said, several things you can do to help yourself. One, any museum worth their salt and who actually wants to acquire your work will work with you to get it in the format they are most comfortable with. New Media art tends to have varying requirements on what needs to be in place to replicate it, what that means, how it works, etc. A museum putting your work into their collection should work with you to define those things and how to keep it working and usable for the long term. That is the museum's *job*.
Second, if you want it to last you need to have original source material. Almost 100% of the time that is what the museum will want. If it's a video they do not want a compressed DVD, they'd rather have the uncompressed DV files or 35mm film if they can get it. If it's an application they want the app, the hardware used to run it, the docs used to create it, etc. Sure, you don't have to give these things up if you don't want to, but you can bet the museum will want as much of the original source and documentation of it as they can get. This will help them down the line when they need to convert the original into yet-another-new-format, and help them catalog the work for later generations of staff (and viewers for that matter, meta data is gold).
Basically, let the museum help you, that's what they're there for. In the meantime, backup, backup, backup, until such time as you have your work acquired by a professional institution.