Drush is a pretty handy tool. I use it whenever I’m working on a Drupal site. I also make extensive use of SSH aliases. It doesn’t seem to be documented anywhere but I discovered that you can combine both.
If you have a SSH alias that might look something like:
Host example Hostname ssh.example.com Port 22 User ssh-user IdentityFile ~/.ssh/example-key-file.pem ForwardAgent yes
Then you can leverage that in your local drush aliases.drushec.php file with something like:
$aliases['example'] = array( 'uri' => 'http://www.example.com', 'remote-host' => 'example', 'root' => '/path/to/drupal', );
Basically you can use your ssh alias as the remote-host parameter and it works exactly like you might expect it to.