Techcrunch features an excellent article today that discusses how the integration of Twitter, Friendfeed, Facebook, etc. reactions into comment threads on blogs can kill the conversation by dramatically increasing comment volume.  Here is the key point:

Instead, there is endless, pointless repetition; conversations emerge, peter out and then re-emerge 50 comments later with new participants who haven’t noticed that the same issues were discussed 50 comments ago.

I couldn’t agree more.  We experimented with integrating Twitter mentions with our blog comments a few months ago and it made our comment threads incoherent.  If you want to track mentions of your article on Twitter or elsewhere, I think the best practice is to use something like the Tweetmeme button and keep comments completely separate from Twitter reactions.