The hunk feature of magit is great; you can easily stage/unstage not only at the hunk granularity but also arbitrary lines using the selection. Being able to easily do that was something I really missed when I moved from darcs to git.
When it comes to magit and TRAMP, definitely the best part is with-editor[1]. This is one of those ingenious "why didn't I think of this?" hacks to let you use your local Emacs as EDITOR on remote machines without having to do SSH port forwarding for emacsclient.
org-mode is a good one, too, but I feel like I've barely scratched the surface there.