Update
When I went to see if Kolachi had responded to my response to his question (i.e., what started this question initially), his question was no longer there and at the bottom of my response was a message informing me that it had been "deleted by Bill the Lizard".
Kolachi's question was about whether Ubuntu Server or Ubuntu Desktop was a better version of Ubuntu for deploying a Ruby-on-Rails application.
So, I'm not allowed to send a perfectly reasonable private message, or comment response, but my valid response can be deleted with no warning and no reason!!!
End of Update
I have a question on SO marked as a favorite and saw a notice that there had been activity on that question. I went to the question and the activity is from a new user (rep of 1) who has asked what I believe is a new question.
My first thought was to send an off-thread comment to the user, but I can't do that - Any way to send a personal message to another user? (of course, still being a fairly new user myself, it took a little searching on my part to find out that it definitely couldn't be done).
My second thought was to comment directly to the user's comment, but I can't do that either because my SO rep isn't high enough (it's a pitiful 24, mostly because I find existing answers to my questions) - How do comments work? . This actually took a lot of searching because it was clear -- from the very question thread that I was in (e.g.)-- that SO supports this functionality, and it was only when I found some other low rep user's support question that I had any idea why I couldn't do what was clearly possible to do.
So what I ended up doing, which, because of the user's extremely new status, I wonder if s/he'll even notice, is I made what I believe is an extremely inelegant "@ username - timestamp" callout at the beginning of a new answer. Of course, because of the ordering of the threads, my response answer comes before this new user's question answer.
Had either of these functionalities existed, I could have clearly and quickly addressed this user, but instead spent at least more than 20 minutes trying to figure out what I could and couldn't do, why I couldn't do it (which I clearly still don't know), how to best help this poor new user, and of course, writing this question so that other users might not have to go through quite as much frustration, for quite as long, and for quite as perplexing reasons.
So, what is the logic behind not supporting private messages or limiting comments to users with a rep over 50?