Only some newer motherboards don't have them, they are becoming obsolete, the new line of legacy free Abit boards do not have PS/2, Serial, Game, Parallel or Floppy connectors anymore.
 
Aside from the floppy disk connector the rest are useless as people upgrade their hardware, printers and scanners are now all USB, joysticks and gamepads are USB, PCI modems do not use serial ports, keyboard and mouses are all USB, and they will work in DOS or Safe mode since the BIOS will automatically emulate PS/2 mode for them. I actually used a USB mouse in Windows NT 4.0 the other day, it picked it up as a PS/2 device.
 
These things are just useless now, they hog IRQs and do not conform to Plug and Play specifications. It is good to get rid of them finally.

USB does exist in "safe" mode but your BIOS must support it. Most do not. Look for "legacy" bios options in your BIOS.
 
Yes, the ISA bus is being phased out. Although it's nice to have Serial/Parallel since that's all that's really needed in most cases to transfer data these interfaces are slowing our computers down. Also there are USB to Serial/Parallel interfaces now so there's really no reason to not upgrade.
 
The floppy connector is also useless since IIRC some BIOS's can boot from USB.

About the only reason I even keep a floppy is so that I can install certain IDE controllers from the get go. That's basically it. If MS would make it so I could install drivers off a CD, I'd have no need for the floppy.

I thought the USB in safe mode was a Windows thing. The less drivers the better in safe mode.