I actually can't think of any such site _without_ comment voting today. Really that's because virtually every social media site now has a one-click way of engaging with comments (notably excluding 4chan). The difference between sites is in whether sorting by score is lacking, available, or part of an inscrutable algorithm; and what other ranking methods are available.
I can't find a single result relevant to the history of voting or user moderation in any search engine. Was Slashdot the first? It and Fark lacked this at launch in 1997;
- Slashdot handpicked 400 users to be moderators in 1999-03[0], and began randomly assigning moderation duty some time between then and the addition of moderation reasons in 1999-05[1]. Metamoderation was added in 1999-09.[2]
- Fark only added comment voting, with separate 'smart' and 'funny' votes, in 2011,[3] making it the only social news site AFAIK without negative votes.