Creating comments via a related section
One approach would be to create a comments channel with an entries fieldtype (with sources checked for any channels that you want to allow commenting; limit set to 1) called 'relatedEntry' (or whatever you like). On your article template, include a for loop to display existing comments relateTo the entry. Check to see if there is a current user, and if yes, include a comments form. In the comments form place a hidden field with the id for the current entry. Something like this:

&lt;article&gt;
  {{ entry.title }}
  {{ entry.body }}
&lt;/article&gt;

&lt;ul class="comments"&gt;
{% for comment in craft.entries.section('comments').relatedTo(entry) %}
   &lt;li&gt;{{ comment.author.fullName }}&lt;br/&gt;{{ comment.body }}&lt;/li&gt;
{% endfor %}
&lt;/ul&gt;

{% if currentuser %}
&lt;form method="post" action="" accept-charset="UTF-8"&gt;
    &lt;input type="hidden" name="action" value="entries/saveEntry"&gt;
    &lt;input type="hidden" name="sectionId" value="2"&gt;
    &lt;input type="hidden" name="redirect" value="{{ entry.url }}"&gt;
    &lt;input type="hidden" name="fields[relatedEntry][]" value="{{ entry.id }}"&gt;

    &lt;label for="comment"&gt;Comment&lt;/label&gt;&lt;br/&gt;
    &lt;input type="text" name="comment"&gt;
&lt;/form&gt;
{% endif %}


name="fields[relatedEntry][] is formated this way because related fields expect an array even if it's only a single related entry.

You could also create threaded comments by creating another related entries fieldtype called parentComment (or whatever you like) and including that as a hidden field in the form as well (you might need ajax or javascript here to help set the hidden field value from the 'comment' link).

To make it a little nicer you could also load the comments form via ajax or reveal it with javascript.

Untested, but hopefully this will point you in the right direction.