I sometimes leave '+1 for XYZ' comments on answers, to emphasise what it is about the answer that I like. These aren't general '+1 Good answer :)' comments, they have an amount of specificity.
Are these comments still discouraged?
It's a grey area where we trust the community to use their best judgment.
As a rule of thumb: if you're on the fence, don't make a comment.
Comments are not intended for long-term storage of important information. But that transiency doesn't mean you can use comments for random, parenthetical asides. If your comment isn't likely to change the content of the post, please do not post it for someone else to clean up.
What this generally means is the default stance toward comments is 'delete on sight' when they come up for moderation.
See Rarity's post:
+1 great question/answer: Yes, we can see the votes. These are only okay if the comment otherwise has substance. If it's useless without the +1 it's still useless with it (same for -1)
We're going to have to trust your judgment on that. Generally speaking, if there are a lot of comments on the post already, or the post is older than a few days old, I would really appreciate it if you erred on the side of restraint, because...
You can read up what Jon Ericson said about comments -- he has plenty more if you search around, but comments are not fun to cleanup.
Though this may seem absurd, it probably takes more time for someone to moderate a comment than it does to make the comment in the first place. That doesn't mean don't make the comment, but it just means that you should be aware that at some point in the future, someone will have to take some time to read through your comment (and others) to figure out what to do with them.
When in doubt, err on the side of silence.
When you do a downvote, it is customary to use comments to explain why, so the author and any readers learn what specifically you disliked about the answer. This tells the author and anyone else what kind of behavior exactly you would like to discourage in the community.
As an extension of this it makes also sense to explain why you upvoted something. It gives the author and anyone who reads it feedback about what behavior specifically you endorse and would like to see more of in the community.
Comments like "+1 for proper formating your answer" or "+1 for finding and linking so many reputable sources for your claim" tell people "Do this too, and you get more upvotes!"
There is, however a kind of +1 comment I see a bit more critical, and that's the "+1 for having the same opinion I have".