This "nothing we can replace it with" sounded wrong to me, so I spent a moment trying to quickly draw on my tablet some possible alternate metaphors for many of the things used in this article, and I came up with these:
http://drostie.org/icons.png
(Disclaimer: my ability to draw is very limited so this looks unintentionally minimalist, because my "boxes" are just squares.)
You could have some convention which says, say, "the present file is a sort of ball or rounded object, the filesystem is a box where we can put our balls, the clipboard is some sort of stack of stuff," and so forth. Phones could look more like mobiles do now, if you put them in a bit of perspective and gave them a keypad. Rather than using the page for a generic document, we have the ball for that purpose, so we use the page instead to indicate printing, since you're converting the ball into a piece of paper.
I think wrenches, magnifying glasses, and binoculars can stay as iconic things -- but since people now use magnifying glasses for "zoom" we should perhaps stabilize on binoculars for "search"/"find". (And come on, I'm not Sherlock Holmes. I'm not trying to find a clue, I'm trying to find last night's homework.)
Email is much trickier; if we don't keep using envelopes, I don't know how we would iconify that.
