If you're running a big site, you may be able to take advantage of the Disqus Single Sign-On System!
WordPress comments can be imported into Disqus using WordPress' WXR export format! Disqus has a doc on WXR importing. The WXR format includes the users' email addresses, which is fantastic because according to this Disqus document about merging accounts:
Guest comments posted with your email address can be claimed at Edit Profile > Merging. This option only appears once you've verified your email address.
So users can reclaim their comments by
- Signing up for a Disqus account.
- Verifying their email address.
- Merging their accounts.
If you allow guest comments, users' comments may be linked if they provide their email address along with their comment. I'm uncertain about how Disqus displays guest comments, however.
Disqus has a separate user table than your blog. Unfortunately that means that your users can't sign into your blog and immediately comment into Disqus. It's trivial to sign up for a Disqus account though, as you probably know, so I wouldn't let that dissuade you.