If patients needs to increase or decrease their dosage, the hospital can do so without changing the appearance of the pills, which could help those with memory impairments.
I can think of other applications for changing someone's dose without them being aware of it. In fact, you could slip them a custom printed pill that looks just like the rest of the pills in their bottle.
Extra Credit: consider the implications of custom 3D printing Drug A in Drug B's clothing. (Pill for Drug A looks like it is a pill for Drug B.)
We won't even talk about illegal pills that look like they are legal pills. Officer, that is just a bottle of tylenol.
Someone could also take placebos that look just like the real thing.
But don't stop there. Maybe you print a pill so that it looks like a piece of candy.
Real Users hate Real Programmers.