for Amiga, Winuae does (partly) with the scanlines and other tweakings in the Filters panel;
Other emulators use them, most notably Mame. But i don't know about Atari emulators using them.
One (imho) feature that miss in Winuae and other games is the possibility to tweak resolution, hue, brightness and contrast in emulation independently by the Windows' display.
That would be useful to play around with this kind of tweaking.