I think the single, most important thing to remember when critiquing a work is to remain true to the author's vision.
I sometimes ask questions before offering feedback. This is mostly to ascertain what it is *exactly* the author's vision is before I begin to think about helping them. Some works are fairly obvious in their direction and intent, and I feel comfortable offering feedback without asking--however, some are more ambiguous--especially those that cross genres. It's fairly easy to decipher what a romance or sci-fi excerpt is aiming for ;) Literary, mainstream, and more 'umbrella' genres are a little tougher.
A lot of times, when I'm working with other writers, if they're having trouble sharing their vision, I often ask them to define their audience. So, if you're not sure what you're vision is for a work, or you're having a tough time figuring out how your work might best be marketed--think of the audience it addresses.
And no, not "Everyone" is gonna love what we write :) If you're having trouble figuring out who the audience is, think of who it ISN'T first. If you have premarital/explicit sex or strong language, there are those who wouldn't touch it with a ten-foot pole. If you write primarily stories about strong women in quirky situations--it's likely not going to appeal to men who would rather get a vasectomy than watch a 'chick flick'. If your story contains overtly Christian themes and is a morality story--athiests and Marilyn Manson fans are likely not going to be interested ;)
When you narrow down the audience, you'll have a much better idea on how to define them, and therefore, can create a meaningful marketing plan that will save you tons of headaches in the future--both for your career and for that feedback that "just doesn't understand my writing."