Thanks for asking this question @saiki. It gave me a reason to revisit atom's packages section and uninstall less frequently used packages. Here are the ones, I use most of the time. :)
atom-beautify : Can't live without it. Cannot see CSS improperly intended.
atom-live-server : This one is very handy. Most of the time I deal with static designs (HTML & CSS), this helps me launch a simple development http server.
close-tags: I hate it when HTML tags don't close automatically.
expand-selection-to-quotes 🏆 : This is the best package. Found it after a lot of search. Helps you select content between quotes using Command + '.
file-icons : I think this package should ship by default with atom. Almost everyone uses it.
git-plus : Helps you do git operations from the Atom' s UI.
git-projects : Shows a list of git projects in a particular folder. Find and open them directly from Atom.