Google Reader recently enhanced Reader's commenting abilities, via an "Options" menu that is present for all conversations about shared items. You can now get a link to the equivalent conversation in Google Buzz, which is handy for passing around a funny thread. If it's your shared item, you can disable comments entirely, if for example the conversation was about a topic whose time has passed.
Additionally, you can now moderate comments within Reader. If the conversation is on an item that you shared, you have the option to remove comments directly. For all conversations, you can report comments as spam.