I only know one way to critique a manuscript, and that’s with a nervous heart.
Critiquing is a serious, sometimes tricky, business and shouldn’t be taken lightly. If someone trusts you enough to show you their work, consider it a privilege. Give the task the same level of respect you afford your own writing, and embrace the idea that you might be unsure of the feedback you’re giving even as you give it.
The important thing to understand is that what an author really wants is an alternate perspective. They’ve probably spent a long time with this story in their head, and now they need to put it in someone else’s hands for a while. Respect their efforts, and do your best to give them an honest assessment of their work.
At the same, though, you need to remember that no two critiques are the same. Each should be tailored to the author of the work you’re reading, and you’ll have to consider both what the writer wants and what they are able to process.