Etiquette for effective workshop comments After a few years of graduate school, I've noticed that I may not be asking questions and making criticism in the workshops in the best way. By "best," I have two goals for comments. The first (selfish) goal is to develop a reputation for being a intelligent, insightful colleague with good comments. The second goal is to effectively communicate my concerns to help others improve their research. Luckily these goals are mutually reinforcing.

Observing others in my department's weekly workshop, the questions that usually get the most attention are those that are phrased quite strongly, even aggressively. 

My tendency has always been to be polite and not try to put someone on the spot about their work. I gently communicate the problems I see with the work. As a result, presenters often do not listen. They brush off the questions as if they are unthreatening and thereof of limited concern.

I do not want workshops to be a threatening or aggressive environment, but it seems like only questions that get the presenter's adrenaline flowing regularly warrant proper consideration and response. Maybe I'm going too soft and I can find a middle ground without being one of the aggressive (sometimes rude) ones.
I am not sure that your questions at a conference are necessarily a major concern. If you look at how science is propagated, conferences are typically a step before publication. Therefore, it is noble of you to think of it as a point where you can provide constructive comments to authors about their work. However, the most critical point comes when work is published and peer-reviewed.

Based on your experience at conferences (which I to some extent share) you can ask yourself the following: Is the author/presenter interested in your comments. If he/she is, then it would be counter productive to ignore your questions. The question-and-answer format, on the other hand, is too brief and fragmented considering the time constraints of a presentation schedule to be the forum for constructive criticism. That is probably also why the more aggressive questions dominate. In the end, there is nothing wrong with approaching a person during a break to initiate a deeper discussion. you will then also get a better feeling if your comments are welcome.

A final thought. I tend to think as the saying: it is sometimes better to be silent and seem a fool than to speak and prove it. You can exchange "fool" by whatever trait you wish.