Speaking for myself, of course. TRAMP (especially with eshell and grep), IDO, magit, effortless buffer splits, org-mode, inline execution of elisp.

I am also rather used to the command set now. To the point that it just feels natural to jump around a file with emacs. ace-jump-mode is also good. Even something as simple as subword-mode is awesome.

Really, TRAMP has been the killer feature for me lately. The way it enhances grep results is ridiculously useful.

I like indent-region and the simplicity of C-x b to switch buffers.

I do think Atom has the potential to really go beyond what emacs has accomplished b/c more people know js/coffee than elisp, but emacs is also a moving target and has become a lot better than it was 10 years go.