Why are EEG markers usually sent over the parallel port?
I think this is for scientists who like to design their own setups. I doubt medical EEGs have a parallel port. You do not always want to sync to a computer. You will often want to synhcronize it to a photodiode, an eyetracker, a tactile stimulator etc. With a parallel port you just plug that trigger to a given pin then you know that everytime your get an integer containing 2^(pin number) you have received a trigger on that pin: for ex. trigger on pin 0 if you are reading 1, on pin 4 if you are reading 16, and on pins 1, 3 and 6 if you are reading 74. Yes, you could read your triggers with a micropchip, then use a serial-USB converter, but that's needlessly complicated and less accurate. USB have surprisingly unreliable timings for a port that can work at such a high baudrate. So it's usually better to synchronize everything to an external input. I usually synchronize an eeg and an eyetracker to a photodiode, then I know they are synchronized perfectly (yet they often have a 1msec difference for some reason).

On top of that, I'm sure there must be some backward compatibility issues. If you are a small lab that has built a complicated setup over the years, you might not want to change your EEG if it means changing your entire apparatus.