My favorite thing I wish they'd told me about emacs: M-x shell Run a shell (or shells) inside emacs. Great for long running apps like servers. You can search back through the output using normal Emacs search commands. For me, one of the killer features of Emacs. Rename the shell buffer to something else to start another shell.
I found that 'shell' mode occasionally got confused, for instance on what the current directory is. I have changed to 'eshell' as my primary shell emulator, one that implements a number of the basic commands directly in elisp. It works quite well, except when running an interactive command which is does not handle well and there are some issues with piping as well.
Generally I like to have bash available so that's why I use shell instead of shell.