pg's comments aren't differentiated in any way, but on discussions of potential new features, I'm very interested in seeing his comments. Even if they don't add on to the ideas being discussed, they're of interest because they indicate possible new features or changes to the site.
Also, username hiding is a good idea in some cases, but I think it's worse overall. It encourages snarkiness, some posters are actually worth looking out for (grellas on legal threads, pg on HN, etc), and it makes back and forth discussions difficult to follow unless you give each user a unique ID per thread. Impersonation can also be a problem. Overall, I think it adds up to more problems than it solves.
Names are important because they allow you to use your own internal karma system (I will read comments from certain people no matter what their score).
One problem mentioned is the overloading of what an up/down vote is - what about separating "good/flag" and "agree/disagree"?
I upvote comments if I am interested in reading them. I'm likely to be interested in reading anything that pg writes because he runs this site. The bar is set rather lower for pg than for any other user and for good reason.