Sweet, after checking Devot-ee (why didn't I look there first) I found a recent addon called 'Custom comment fields' (http://devot-ee.com/add-ons/custom-comment-fields) which allows you to add some simple custom fields (Text input, Textarea, Safecracker File) to EE comments module posts. I then used this as a way to add the ability for logged in users to specify if there wished to post a specific comment anonymously.
I added a new custom field using this addon called {comment_anonymously} and then set this as a checkbox field in the {exp:comment:form}
<label>
<input type="checkbox" name="comment_anonymously" value="y" />
Post my comment anonymously
</label>
Then in the {exp:comment:entries} loop, I used a conditional on the custom comment field to display the users name or not:
Posted by
{if '{comment_anonymously}' == 'y'}
Anonymous
{if logged_in_group_id == '1'}
(<em>{name}</em>)
{/if}
{if:else}
{name}
{/if}
Note that I've also placed in a conditional for if a Super Admin is looking to show the users actual name for easy verification.
Cheers
Brendan