Have a rich Atom environment for HTML/CSS/Javascript/PHP usually means: test a lot of packages to find the ones that provide top functionality, play nice with Atom and are compatible with each other. This is a list of packages I decided to keep, others I'm testing and a couple I want to explore in the future.
Wordpress API -- https://atom.io/packages/wordpress-api
Atom Drupal -- https://github.com/favish/atom-drupal
Atom Bootstrap3 -- https://atom.io/packages/atom-bootstrap3 -- Bootstrap 3 Support with snippets and autocompletion.
Linter -- https://atom.io/packages/linter
Linter-csslint -- https://atom.io/packages/linter-csslint
Linter-jshint -- https://atom.io/packages/linter-jshint
Linter-less -- https://atom.io/packages/linter-less
Linter-php -- https://atom.io/packages/linter-php
Linter-sass-lint -- https://atom.io/packages/linter-sass-lint --> Nodejs version
Linter-bootlint -- https://atom.io/packages/linter-bootlint
Linter-scss-lint -- https://github.com/AtomLinter/linter-scss-lint --> requires Ruby
Pigments -- https://atom.io/packages/pigments
Minimap -- https://atom.io/packages/minimap
Minimap Find & Replace -- https://atom.io/packages/minimap-find-and-replace
Minimap-highlight-selected -- https://atom.io/packages/minimap-highlight-selected
Minimap Linter -- https://atom.io/packages/minimap-linter
Atom HiDPI / Retina -- https://atom.io/packages/hidpi --> perhaps problems with Minimap?
Merge Conflicts -- https://atom.io/packages/merge-conflicts
Dockblockr -- https://atom.io/packages/docblockr
Remote Sync -- https://atom.io/packages/remote-sync
Autoprefixer -- https://atom.io/packages/autoprefixer
Atom Beautify -- https://atom.io/packages/atom-beautify
Aligner -- https://github.com/adrianlee44/atom-aligner
Aligner CSS/LESS -- https://github.com/adrianlee44/atom-aligner-css
Aligner SASS/SCSS -- https://github.com/adrianlee44/atom-aligner-scss
Terminal Panel -- https://atom.io/packages/terminal-panel
Project Manager -- https://atom.io/packages/project-manager
Git Log -- https://atom.io/packages/git-log
Git Time Machine -- https://atom.io/packages/git-time-machine
Atom File Watcher -- https://atom.io/packages/file-watcher
Atom Material UI -- https://atom.io/themes/atom-material-ui
Jonikorpi Atom -- https://github.com/jonikorpi/jonikorpi-atom-theme-one-ui
Atom Material Syntax -- https://github.com/silvestreh/atom-material-syntax
Leche -- https://atom.io/themes/leche-syntax
Qcolor -- https://atom.io/packages/qolor
-- semantic highlighting to your SQL queries by matching tables to their aliases.
GIT Plus -- https://atom.io/packages/git-plus
Git Tree Status -- https://atom.io/packages/tree-view-git-status
Quick Editor -- https://atom.io/packages/quick-editor
Atom Sync -- https://atom.io/packages/atom-sync --> experimental
Tool-bar -- https://atom.io/packages/tool-bar
Atom Beautify -- https://atom.io/packages/atom-beautify
Atom Lupa -- https://atom.io/packages/atom-lupa
Bezier Curve Editor -- https://atom.io/packages/bezier-curve-editor
Editorconfig -- https://atom.io/packages/editorconfig
Autocomplete+ Providers
Atom Ctags -- https://atom.io/packages/atom-ctags
Atom-ternjs -- https://atom.io/packages/atom-ternjs
Atom-Hack -- https://atom.io/packages/atom-hack