The origin of the term is uncertain, but it may be derived from Harvard University Cruft Laboratory, which was the Harvard Physics Department’s radar lab during World War II. As late as the early 1990s, unused technical equipment could be seen stacked in front of Cruft Hall’s windows. According to students, if the place filled with useless machinery is called Cruft Hall, the machinery itself must be cruft. This image of “discarded technical clutter” quickly migrated from hardware to software.
Cruft may also be a play on the old typeface form of the letter “s”, rendering “crust” as “cruſt”.
Another possible origin is that the word evokes the words crust, fluff and scruffy. The latter word is the source of similar words in Jamaican English such as cruff, meaning scurfy, coarse or uncouth.
From Wikipedia: http://en.wikipedia.org/wiki/Cruft