Read the entire piece through once to get a general impression of the work. Don't skim, but avoid laboring over specific elements of the piece. If you see an occasional spelling error or typo, go ahead and mark it. If there are numerous mistakes throughout the piece, just add a general request for a spell check at the top of the story.
After the first reading, write a short paragraph giving your initial impression. Keep your comments constructive. If you found your mind wandering during the story, don't just remark that you were bored. Find sections that held your attention, and suggest the writer keep that pacing throughout the piece, pinpointing the sections that could use some work. If the humor in the piece fell flat, find the author's strengths (action, dialogue, description, etc.), and suggest leaving the humor out to let those strong points shine through.
Read the piece again for continuity, character development, dialogue, descriptive passages and plot points. Make notes in the margin (or in a word processor file, if reading online, noting the page and paragraph in question before each comment) as you go. Note your favorite moments; when you felt lost in the plot; continuity errors; and uneven pacing.
Review the paragraph you wrote after your initial reading, adding any specifics that might clarify your first impression. Again, keep it constructive. Note the strengths and weaknesses of certain characters, or surprising plot twists and why they did or did not work.