The base plugin for linting in Atom is linter. It's a modular approach to the linting problem. That plugin is the engine where subplugins run.
For great autocompletion in Python projects I use autocomplete-python, it's powered by Jedi. It requires some per-project configuration but it works like a charm.
I work a lot with Django, but the only plugin I really need it's proper syntax highlighting for its templates, which I achieve with language-python-django-templates.
My personal choice is JSLint, but I want to give ESLint a try someday.
Minimap provides a preview of the file in the scroll bar, it's great for quickly scrolling to the section of the file you want to edit.
File-icons really helps figuring out which file is which without needing to look at the file extension, and makes the editor look pretty damn good too.