When you sit down to write a critique, the first thing you want to do is read the piece with a critical eye and search out both trouble spots and indications of strength. Here are some areas to consider:
Tension -- the state of uneasy suspense that draws the reader, word by word, through the story. Tension is created through questions raised but not answered (immediately) and through conflict, but also on a micro level through word choice and sentence arrangement. Think of it as a cord running through every word, every paragraph. Are there times when it tightens appreciably? When it goes slack, does that happen at an appropriate time and does it tighten up again soon (good), or does it remain slack for long periods? (not good).
Conflict -- Story conflict has been defined as the lifeblood of fiction. Without conflict, there is no story, only a string of random events. Conflict manifests when characters struggle against other characters, or against some outside force, or against themselves. A character must want something, badly, and/or fear something, badly. What he does in response to his desires/fears is what develops the story; how he resolves the conflict is what ends it.
Emotion -- Character emotions should be clearly shown, otherwise they will appear robotic. A good writer does not write with emotion; rather, the good writer creates emotion in the reader. They do this by careful revelation of a character's thoughts and motivations.
The opening hook -- A story should open with some event, character, description, or narrative thread that entices the reader to continue. No matter what form it takes, it must arouse the reader's interest.
Plot events -- The events that arise as a consequence of a character or characters decisions. They can also be outside events that pressure the characters into action. The question you want to ask is -- are they realistic? Intriguing? Logical? Are shown or are they told?
Setting -- A fully realized setting adds texture,context, and credibility to a story. A dull setting will drag a story down.
Structure -- Stories can be told in any number of ways, from a linear storyline to frame stories to stories that rely on frequent flashbacks. They can be told from one character's perspective, or many. What's important is that the structure work--i.e., it mustn't cause confusion, slacken the tension, or induce boredom in the reader.
Characters -- Should feel real, not flat or cliched. Good characters will seem larger-than-life--they are like us, yet they take actions, make choices, or say things that we only dream of. Characters should be real enough to be unpredictable, to have secrets. They will not be stock, but unique. They should want things badly and feel emotions strongly. We should be able to relate to them.
POV -- the viewpoint from which the story is told. Whether it's first person or third person (very few stories are told in second person), the POV should be true to the character's perspective and switches should not be jarring or confusing.
Dialogue -- Should be realistic sounding, without all the stutters and hesitations that mark normal speech patterns. Story dialogue should also be purposeful, not idle chit-chat. Its must advance the story and develop character. Good dialogue is confrontational. It is also often oblique -- i.e., it does not answer questions with an obvious yes or no, but proceeds through indirect responses.
Flow -- This is one of the hardest things to accomplish in writing, but when critiquing, it's fairly easy to spot when it's snarled up. Good flow is when things happen in the right order--not just events, but actions and reactions, dialogue and thoughts. It is description inserted where it enhances rather than distracts. It is tension that rises to just the correct degree and is either resolved or left hanging at just the right place. It is the logical, inevitable progression of one sentence/paragraph into the next. When flow is done right, the prose will read smoothly and the story will proceed without a hitch. When it's wrong, there will be bumps and digressions along the way.
Voice -- This develops from word choice, style, and a writer's own talent and experience. Some writers have a distinctive voice and others don't. It's not something than can be critiqued, except to point out where it seems inconsistent. A critiquer should never try to alter a writer's natural voice or rewrite passages in her own voice.
Clarity -- Lack of clarity can manifest anywhere from jumbled syntax that makes sentences incomprehensible to events not clearly described or important information left out. Anything, IOW, that confuses the reader.
Credibility -- Are the characters' actions believable? Has the writer done accurate research, or is the work filled with anachronisms and unlikely scenarios?
Language -- This covers everything through word choice (are words used correctly and is the best word used?), sentence structure and length (is it repetitive or varied?), supporting words (adjective and adverbs. Too many?), dialogue tags, overwriting, underwriting, metaphor and simile, and freshness. The latter is especially important--if writing lacks freshness, even a good story can feel dull and lifeless.
Grammar -- If the work is rife with mistakes, point out one or two of the most glaring errors, but also suggest the writer study up on the rules.
Reader engagement -- Bottom line, were you drawn in? Did you want to read more? If not, the reason probably lies somewhere in the above list. Go track it down.
A few Do's and Don'ts of Critiquing
DO choose two or three major problem areas to address.
DON'T exhaustively critique every sentence and every problem. This can be overwhelming and discouraging to emerging writers.
DO mention any recurring grammatical or punctuation errors.
DON'T try to fix them all. Instead, suggest the writer research solutions.
DO suggest possible changes or remedies to problems, if any occur to you.
DON'T rewrite for the author, unless the author indicates that is acceptable.
DO comment on strengths.
DON'T be overwhelmingly negative.
DO be honest.
DON'T be overly picky. Or personal. IOW, critique the way you'd like to be critiqued.
Finally, some links to articles on critiquing:
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Edited Oct-10 by Beth S/SL-Writing Biz | 
