I am running drush site-install and I want to install d6 but d7 is default, how to I specify the Drupal version?
Usually I use
drush dl drupal then cd into the drupal directory and then
drush si [other parameters].
That means, when you download drupal core you need to specify the version at that time -- not during site installation (which is just running the files).
You can do that by appending the version onto your dl argument, for example:
drush dl drupal-6 or
drush dl drupal-6.x