Decide which modules to enable / disable in make file I have a make file in which modules are downloaded, but how do I decide which ones are enabled?
Drush make only downloads projects; if you want to enable some modules, you must do that with an installation profile.  An installation profile contains a make file, plus some code to configure your site.

If you're using Drupal 7 and would like to create a starting installation profile from an existing site, see http://drupal.org/node/1368242.  There is a patch there that will create a profile for a D7 site.  The issue is marked "needs work" because the code templates for D6 are not in place yet.