As far as emulated scanlines and clean pixel representation, M2 ,does this very well. You have the option of 1:1 pixel with scanline and then with or without bilinear filtering.
Sample images from NeoGeo Station on the PS3:
They have these same options on the Sega Vintage Classics (Super Hang-On, Revenge of Shinobi, Alex Kidd, Wonder Boy, Toejam & Earl, etc..), Capcom Arcade Cabinet.
I don't care for the crazy glowing and saturated color effect that Capcom uses on Final Fight Double Impact, MVC, Dungeons & Dragon's Mysteria... I've never seen an arcade monitor that looked like that unless it was damaged and I'd rather not emulate a damaged display.
I also like the vector emulation on MAME. The slight burn in and light "trails" is a convincing effect for non-vector displays.