They're nice for hobbyists because they bridge the digital<->voltage domains really easily, so you can just hook up wires to the pins and feed them into whatever you're building, rather than having to use a fancier microcontroller interface. But yeah it's getting to be more of a hassle that e.g. a typical laptop won't have one anymore.

In the past I've also used audio line-in/out as a simple two-channel (each way) I/O interface, but that runs into more problems with drivers getting in your way (buffering things and whatnot) than parallel ports do.

They're popular in the CNC world, yes. For instance, the recently Kickstarter-funded MyDIYCNC project also natively interfaces through the parallel port; Stephen McGloughlin, who's behind the project, is building an USB interface for it from scratch.

The main issue seems to be the timing with controlling... parallel i/o lines. From http://www.cnccookbook.com/CCBreakoutBoards.htm :

While there are boards the purport to simulate a parallel port with a USB connection, most of them don't work for CNC applications. The reason is that they are not high enough performance to maintain the exact timing relationships needed to produce a clean pulse train to control multiple servos or steppers.