Ethier port is fine, however be warned that many PS/2 KVMs will only support the plain-jane parts of the PS/2 protocol, so any extra buttons aside from the standard 3 on your mouse may no longer work. I've had this happen many times. You would not have this issue with a USB KVM......
As for the USB vs. PS/2 debate...
On PS/2: Your PS/2 controller samples movement data coming from the mouse anywhere from 20 to 200 times per second (Hz). The default sampling rate in 9x OSes is 40hz, default in Windows 2000 is 60hz, and the default in XP is 100hz. 2k and XP both allow you to change the rate from 40hz to 200hz via the mouse's Device Manager properties window. 9x requires that you use a thrid party tool. (like PS2Rate)
On USB: Your USB Host Controller polls input devices (KBs, Gamepads, Mouse, etc...) 125 times per second for data. This rate is set and cannot be changed.
Could you actually notice a different between a USB mouse updating 125hz and a PS/2 mouse at 200hz? I highly doubt it....
Use whatever port works best for you!