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 [edit] 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?](