I mainly use the MySQL GUI tools. This allows me to easily see the results in a table as well as to quick edits and bookmark frequently run queries. This suits my needs far better than the command line.
I remember when I used to do this on Oracle DBs years ago I could put variables in the query itself, so that when running the query I got prompted for the variable.
e.g.
select email from users where login = [VAR]
And when you run the query the system prompts you for VAR and you can type in john_smith14 and it executes the query. This is really useful for adhoc queries which you run a lot.
Yes I know using shell scripts and the command line this could be done more easily, but for several reasons aside from this, shell scripts are not a good solution for me.