I am rarely seeing a "Reply" option in the comments under YouTube videos. It is there for a few upvoted comments, but for 99% the reply button is missing! For example, see the comment section of this video: https://www.youtube.com/watch?v=raLkw3_IIFc. You can only reply to the two top comments:
Here is a nice report of the problem from the last year https://www.youtube.com/watch?v=-MuofdTPhEA. Has there been any solution/workaround found since?
Best Answer
If you notice, on the new comment (6 days old) you can reply on and other comments (1 year old) you can not. This is because YouTube have changed their commenting to use Google+ profiles.
So new comments are being posted by linked Google+ profiles + enable replying to them. Others don't have this ability anymore.
Frustrating, I know.
Some extra read here.