Here is an example of waterjet cut logos in computer cases:

http://www.customwatercuts.com/index.php

In a production environment, it would be pretty reasonable to cut the
sides of the case, provided you don't have a lot of different points
that need piercing (say limit the number of pierces to under 10 or so).
Since computer cases cut like butter, the cutting would be on the
order of 30 seconds to a few minutes each (or $1-$5) depending on the
complexity and number of pierces.

For high production, this is probably a bit too expensive, but for runs
of say 10 to 1000 cases, it may be reasonable.

For low volumes (1-10 cases), drawing the artwork and making the tool
path and setting up the machine and such add a lot of cost compared to
the very quick cutting, which is why a place like the above charges
much more money.

Carl