Best PC interface for simple custom hardware
The parallel port is great when you're using Windows 98 or DOS.  All modern Windows operating systems have drastically changed how the parallel port interface works making it almost impossible to interface with anything other than a printer.  And the parallel port is basically obsolete at this point anyway.  Also, it's basically impossible to do any precisely timed control from a general purpose computer.  If your target is milliseconds, it's not too bad.  But if you want to get down much lower, it gets very, very hard to do so reliably.  You're better off sending high level commands to a microcontroller or similar.  I would get an Arduino if you have never used a microcontroller before.  

If you want to do any serious interfacing with hardware, you're probably going to be using USB.  If you need RS232 serial, get a USB to serial converter chip.  These are readily available from companies like FTDI and Exar.  Most of the boards I make have a header I can plug a small USB-serial adapter board in to, or they have a USB-serial chip on board.  Ethernet is another option if you need higher speed communication, but supporting Ethernet on your device is usually quite a bit more complicated than a simple serial interface.  It's also possible to interface with PCI, PCI express, and Serial ATA if you really need the performance.  

Edit: I can no longer recommend FTDI with a clean conscience without also mentioning that FTDI has released a driver which contains code to intentionally (and likely illegally) destroy "counterfeit" FTDI chips.  See http://www.eevblog.com/forum/reviews/ftdi-driver-kills-fake-ftdi-ft232/ and http://www.eevblog.com/forum/reviews/ftdi-driver-kills-fake-ftdi-ft232/msg535270/#msg535270 for more details.  If you are considering using FTDI, then you need to weigh the risks of your devices failing in the field due to this driver, either due to counterfeit chips slipping into your production somehow or some issue with the counterfeit detection in the FTDI driver.