Whereas if you reply, your reply forms a new post. This happens whether you use the reply button in the upper right corner or the small reply button underneath a post.
New posts in a topic bumps the thread up to the top of the active topics, comments do not. I prefer using them like this: when replying to the original topic, I use reply. If someone comments on my reply, I continue using comment to discuss with them. To reply to another person in the thread, ie not the original poster, I use comment. And also if I simply don't want to bump up the thread for some reason.
Hope this explains it!
If you reply, the topic will be marked as watched for you and is shown in watched topics.
If you just commend, it doesn't. If you want to watch, you have to activate it.