User can select it from drop-down list of refresh rates that your GPU/Dispaly support:

Nestopia had "auto" refresh rate function in fullscreen depending of region.
For NTSC, emulator try to set 60 or 120 Hz, prefer higher value, if hardware supported it.
For PAL/Dendy, emulator try to set 50 or 100 Hz, prefer higher value, if hardware supported it.
It was really nice when i had CRT, which supported 60-75-85-100-120Hz:

I guess nice idea is combine this methods.
To make an separate "requested refresh rate" options.
Two drop-down menus where user can set prefferred hardware refresh rate: one for NTSC, second for PAL/Dendy
Fortunately, lastest modern LCD displays have wide range of refresh rates native support, usually 50-144Hz
as well, as AMD FreeSync or Nvidia G-Sync technologies for automatic refresh adjustment.