It's worth keeping two semi-contradictory ideas in mind when interacting with new users:
Different people, and people from different backgrounds, will read things in different ways; a comment meant to be succinct might come across as dismissive, or emphasis might be interpreted as shouting.
Some people are very sensitive and there's not much you can do.
With a new user you don't know which of these applies (if either). I try to do the following to (I hope) improve the chances of a good experience:
I try to start off my first comment to a new user with some sort of greeting; while some find it superfluous or even noisy, others see it as welcoming.
I try to acknowledge that expectations might be off -- "we're a little different from other sites" and similar language can make the user less likely to feel blamed.
I try to avoid all-upper-case for emphasis because it can be seen as shouting even though that's not what I intended.
I try to link to relevant resources (like the on-topic list in the help center).
I try to suggest improvements rather than using critical language -- "you could improve this by X" or "could you  to add...?" instead of "this is off-topic" or "you need to X".
Sometimes, no matter what you do the user gets upset. We can't make everybody like us; we can only do our best to provide an environment where someone who wants to be part of a site like ours can do so.
Related (broader than just comments): What are the most effective ways to guide new users?