It wouldn't hurt for both. In fact, blog commenting with links to articles and links inside the article pointing to your site is a great resource for quality links around your domain. I would split the process in two methods.

When commenting split between both methods:

1) using your article links
2) using your domain or inner pages (content on your site)

Yeah, I would agree with DesignerJack, mixing it up is the best answer

I agreed with designerjack. By using the links from the great content, main site and its sub pages is an effective ways to gain quality backlinks.

It depends on where blog commenting lies in your overall backlink strategy. If it is the only thing that you are doing, then it should definitely be both.

If it is just a part of your strategy, then take a look at where you are currently linking to and fill in the gaps. One of the benefits of blog commenting is because it can be done fairly quickly, you can change the pages that your linking to whenever you need to give them a boost.

Main keyword > Home Page
Sub keywords > Inner pages

That's my simple formula for all backlinks

mix different urls and when possible use dofollow blogs, though high pr sites do pass authority even when nofollow and good writing will send targeted traffic right from the comment.

Make some variations. It looks natural.

Petter Hedman