I agree with bjb, and have similarly flagged "+1" and such comment that was declined, which surprised me. I know that our comments are chattier than other sites, and that's fine within reason; but I don't believe our comments should be this level of chattiness. If you agree then you should push the "vote up" button, not leave a comment. (and I think "my speculations precisely" means "I agree", not "I think this is a speculation", which is almost the opposite in feeling).
In general, we use comments for more of a discussion forum here, and I think that's something that in the long run will hurt us. The comment discussions end up containing a lot of information that doesn't make its way back into the answers in some cases, and that's where the problem really is: in the long run, the answers need to contain all of the useful information. However, beyond that, assuming we keep more-or-less the discussions-in-comments that we do now, the lone "+1 agree" comments and such should still be removed, because they do harm to the rest of the discussion.
The Stack Exchange platform isn't made to make comment discussions really work; it hides all but a few comments, and can feel sort of at random which, so it's hard to follow the whole discussion when it has many comments. They're fine while the discussion is in progress, for the discussers; you get reply notifications and such. But days afterwards, they're not very readable. As long as the important information from the comments gets imported to the answer that's not a big deal - but if it doesn't, then having a lot of little random comments is very unhelpful, and it doesn't always get imported.
Moderating comments a bit more would be a reasonable middle ground, I think. Don't use comments to show agreement; those should be deleted. Comments should be used for clarifications or asking questions about the question or answer. Nothing wrong with a (even a long) discussion in the comments, as long as the comments are useful. But also don't use comments to answer the question; encourage people who 'answer in comments' to convert the comment to an answer proactively, at least once they've clarified things sufficiently if that's why it's a comment.
Either way I think we should discuss this, and in general our attitude on comments, either here or in a new question, as a community. It's one of the things that differentiates us greatly from other Stack Exchange sites, and I think it's worth discussing whether the current approach or something different is appropriate.