Can handle up to 5.5V on SIO pins, regardless of the microcontrollers maximum supply voltage (this is due to no top ESD diode).
Sink/source more current than GPIO
Can have programmable drive voltage levels
SIO pins cannot:
Act as analogue I/O. This means you cannot connect them up things like the ADC, VDAC, IDAC, e.t.c.
Cannot act as LCD I/O.
Some SIO pins also have fixed-hardware I2C peripherals connected to them. In my experience, SIO pins also tend to use a little more power than GPIO, it seems that their input buffers consume more current.