MiSTer FPGA Forum

What are the advantages of using a CRT VGA computer monitor at, say, 1600x1200 versus 640x480? Is it only the higher resolution? If so, is there that much of a picture quality advantage to displaying the content at higher resolutions?

When using MiSTer on a VGA CRT there is no advantage or disadvantage in displaying a the image at 640*480 or 1600*1200 unless you start to use the filters.
Most systems run in resolutions below 640*480 anyway so the picture needs to go through the scandoubler to be displayed on a VGA monitor at all. The higher resolution of 1600*1200 won't result in a higher resolution of the source image at all, because this still is something like 320*200 (for most cores).
When using filters it may look different.
It may look different, because your screen is capable on a technical level to display 1600*1200 but not very good at it. This can be the case when the shadow mask of your screen isn't really suited for such a high resolution, but I think most CRTs you will find today still running should have no problems displaying 1600*1200 in good quality.

If you have a VGA CRT monitor, there is no need to set a resolution for most cores. By setting almost all cores will create a 31KHz (or higher) signal, that will be shown on the CRT.

For the few cores that lack scandoubler support and the arcade cores that are in vertical orientation, you can use with a resolution of your choosing. I tend to do a custom resolution for each core that allows me to use integer scaling using https://arachnoid.com/modelines/ to get a Linux modeline and https://morf77.pythonanywhere.com/ to convert it into a MiSTer modeline.

For the vertical arcades, the picture need to be rotated, so the X resolution becomes Y. Higher resolutions are often needed to get 2x or 3x integer scaling and look much better than squishing the picture into a lower resolution using non-integer scaling.