I'd like to run Ys 1&2 Complete (PC) at a resolution higher than 640x480 and all my searching keeps turning up empty. I know the configuration utility that comes with the game lacks any choice in resolution but there are usually ways around that such as editing the game EXE with a Hex Editor, much like I did to get a proper 16:10 aspect ratio for both Ark of Napishtim and Oath in Felghana.
And I do understand that this would only scale the image just like my monitor is currently doing, but when the scaling is done on the GPU, post-processing can then be enabled so any upscaled image can be smoothed etc. This simply cannot be done when its the display that is doing the scaling.
It may be possible just depends on how much work you want to put in. I did something similar to Chantelise. I did it to make it wide screen but also made any resolution possible instead of just the three that came stock. It took a bit more than a hex editor though.
You could try just searching the exe for the hex values for the resolution. They should be somewhat near each other but there are probably lots of false positives. The values would be 0x8002 and 0xE001. That may not be enough though, and they may be obscured. Maybe you'll get lucky though.