OK, I guess I had assumed that this wasn't a PC monitor. If you hook a PC monitor up to a modern PC, it should hit it with native res (including on the analog VGA input) by default, assuming the EDID data is correct (which seems to be a big assumption). This is how you SHOULD drive it if using a PC and emulator since it avoids repeated scaling. If you are unable to do this, many, though not all, PC monitors do have an aspect ratio option. Some will automatically set the aspect ratio based on detected horizontal resolution on the assumption that the pixels are supposed to be square (since Windows makes this assumption, anyway - much to the chagrin of people like myself who have 16:9 TVs with a native resolution of 1024x768).
I was operating on the assumption that this was a TV or arcade monitor being fed something from a console or arcade board. In those cases, you'll need to do what I said.