ok since the atari emu's do not seem to be getting any loving. I'll go ahead and dive in with a first post.
7800 emulation does exists in MESS, although it may be too much of a "mess" to deal with. The 7800 is pretty much backward compatible to the 2600. Kinda like the PS2 to PS1. So I decided to mention this here.
No save states.
Doesn't properly set the A/B difficulty switches that you select in setup.
Record/playback does not seem to work properly (not that I use it much). The only game I tried it on was megamania.
No ability to access the black & white/color switch. I know this seems a moot point, but some games rely on it as controls (for example to bring up a star map).
I'm sure if I poked around a bit I could find a few more odds and ends, but these are the ones I've run across.