Until all emus support 29KHz external monitors, the best way to enjoy emu graphics is to use a fullscreen 640x480x50Hz or so resolution, synced, double the graphics, and then, to avoid blocky chunky pixels, use scanlines. Preferably, increase gamma/intensity to melt the lines a little bit together.
If you prefer to play in a window, set a high resolution, 100 Hz. Then you can have blocky pixels without them getting so unforgivingly blocky and huge. Or use 25% scanlines.