Checkbox list for content type in drupal 7
You're right...the CCK module has now been incorporated natively into Drupal 7, so you would use that.

Just visit http://mysite.com/admin/structure/types/manage/CONTENT_TYPE/fields to add the fields to your content type in pretty much exactly the same way you did using CCK in Drupal 6.

EDIT

Sorry I understand your problem now, the node reference and user reference modules aren't part of the default field system in Drupal 7; you just need to download and install the References module and then you'll have the "Node Reference" option in your field type drop-down like you're used to seeing.