I'm not sure if this will work, but have a look at the query below, I added the "AND items..." section:
SELECT * FROM items LEFT JOIN user_items ON
items.item_id=user_items.item_id WHERE user_items.userid='$userid'
AND items.item_id NOT IN (
SELECT primary_id FROM user_equipped_items WHERE userid='$userid'
)
This will exclude all item_id's that is found in the user_equipped_items table. I'm also not sure if primary_id is the correct column?
To come back to your original question on how to join, it gets complicated when you left join and then want to join another table to that table. Let me know if the above sql works, if not I'll rethink the query.