The whole purpose of a workshop, whether as part of your MFA program or in an independent writers group, is to help the writer with his/her work and development of craft. My basic rule for any comment is if it's not useful to the writer, then keep it to yourself. Avoid delving into the writer's psychology or personal life ("Your characters are having trouble with their marriage; is this because your own marriage is falling apart?"), and try to remember that just because something is outside your own realm of experience doesn't make its existence impossible.
But don't listen to me. Listen to Meir Ribalow. He runs a playwrights group at The Player's Club in New York City, and he begins every session with a recitation of his rules. I think these rules are genius, and everyone in every workshop on earth should use them. So here they are:
All comments have to be constructive. No trash talking allowed.
You have to comment on the work in front of you, not what you would have written if it had been your idea. Even if you think your idea is better.
No invidious comparisons. Saying "Sophocles did this better" isn't helpful.
Don't try to rewrite for the author. The author can do that him/herself. Just point out the areas of concern.
So what has your experience been like? Got any workshop horror stories? Or rules you think should be added to the list? Comments, please! (Constructive ones, of course.)