Whats the best practice? Basically I generally have hundreds of comments per article and I NEED to paginate them, but in terms of SEO how do I go about doing it? I don't want paginated URLs (example.com/article/comments-page/34) being indexed and I'm not sure if I want to index the actual content of the comments. suggestions?
What CMS are you working on? It will likely have a plugin or something to do what you need. For not wanting the urls indexed, you can simply add noindex and nofollow to them all by default, that should do the trick
It is actually a bespoke system so no plugin is available But would I really want to just not index all comments past the first page?
But it won't work... I don't want to not index pages, I want to index them I just don't want duplicate content.
Give this a read http://searchengineland.com/five-step-strategy-for-solving-seo-pagination-problems-95494 and look into getting the guys that coded your custom cms to add rel=”next”, rel=”prev” along with rel=”canonical” tags for all your pagination urls.