How to identify hung queries, their importance, and then take action using command line?
There are two utilities that you may want to look at:

1) mytop

2) innotop

They are, as their names imply, the MySQL equivalent of the "top" system utility.

They won't help you figure out how "important" a query is because this requires deep knowledge of the system issuing the queries.

For a deeper, longer term (rather than real-time, catch-it-while-it's-running) insight, you can capture the slow log (adjust long_query_time appropriately to your opinion on what is problematic), and analyze the slow log using one of the following two tools:

1) mysqldumpslow

2) pt-query-digest

These will give you insight into which query "templates" are the ones consuming the largest amount of the server's CPU time.

When you outgrow the capabilities of the command line tools and you find you need a deeper long-term insight, I suggest you look at PMM (Percona Monitoring and Management), it is an extremely useful took for identifying performance issues on database (and not just database) servers.