The borders on comments are fairly ugly, and far too thick.

I refreshed this page, and only the new comments had the thick, lime green border, so it seems to be a way to show which comments got posted since one last viewed the page. Anyway, it looks a bit off to me too; maybe it'd work almost as well if it had the same thickness as the normal, thinner border? The lime green colour would stick out less if the border weren't as thick.

Perhaps they [the thumb icons] can be shrunk a bit and placed in the title line of the comment, along with the permalink and reply icon?

I think this is worth a shot. (Also open to Alicorn's suggestion that the icons go back to being words, in which case they should probably stay at the bottom of comments.)

You could potentially hide all the icons unless you're mousing over the comment, to avoid clutter.

Count me as a vote against that idea.