What you are referring to is link triangles. It's black hat, and punishable.

You clearly want to perform a link exchange, but you know the links would be discounted. In order to manipulate the system, you link to another site to avoid the link exchange.

The bottom line, it is a search engine's job to determine which web pages are the most relevant and reliable for a user. Links are a large part of their calculations. Anything you do to muddy the waters and make it difficult to determine whether a link occurs naturally, or it is paid for / exchanged, it black hat and would be subject to consequences upon discovery.

Very information reply as always EGOL. Any rough estimates on how long for the full link's effects to be in place? 4 weeks?

I wouldn't go so far as to call the extra links spam. They are not helpful to SEO. They just add extra links to your page.

If you sincerely believe they are helpful for users, then leave them. Otherwise, I would recommend removing them.

I understand the logic behind blocking removing the variables. They are a lot of extra links on the page which some webmasters might prefer to manage.

What I would prefer is to reform the link so it was something like: http://noahsdad.com/treadmill-training-progress#replytocom=22729

I am guessing the "respond" portion of the URL acts as if someone pressed the reply button which seems unnecessary. If someone clicks the link whether in search results or otherwise and is taken directly to the comment, they should be quite happy. If they wish to reply they can hit the reply button.

Google ignores anything after the # character in a URL. Therefore Google would see these as simply a link to the page which should already be indexed.

Perhaps you can ask Yoast about his thoughts.

Regarding the new pages instead of posts idea, do you have a link to share?

Regarding the comment url, the page with the comment should be fully indexed either way. By changing the link, you are helping search engines better understand your site. The comment links do not represent a new page or new information.

Google clearly understands WP sites exceptionally well. I am confident you can choose various options and they will still understand those links represent comments. With that said, I would still go with Yoast on this one.

Actually, SEOmoz does it too. Take a look at their blog comments.