Questions that should be safe to ask

The safest and easiest question to ask is probably, "How are you planning to follow up on these results?"
This may or may not be a particularly compelling question for the audience, but it is likely one that the speaker has considered so it provides an opportunity for them to speak a bit more within their expertise about projects that are ongoing. You'd only ask this if they didn't already answer it during the talk.

What follows are some examples of other strong questions.
I think the first three are the strongest:

These all give a presenter permission to speculate.
In fact, you could specifically ask them to speculate; this takes some of the pressure off. That way, the speaker is able to riff and they are not held accountable for the answers since they are speculating.

These are not challenging questions that come across as aggressive.
They can call be worded in ways that invite carefree, low-stakes speculation, which has the potential to bring forth answers that are fun for the speaker. These could become aggressive if worded inappropriately, but they are easy enough to word kindly.

Questions that flip something around:

You suggested that X directionally relates to Y; what if Y directionally relates to X?
You suggested that agreeableness promotes helping; what if helping promotes agreeableness? Could the apparent effect be reversed?

Questions that expand to a wider group:

Your sample was undergraduates; what would you predict about your results in older adults, maybe people in their seventies? what about preteens? Would you predict that your results would hold or do you expect that they would they be different?
Note: You would pick the comparison-group based on the subject-matter
Your sample was American; would you expect similar findings if you attempted to replicate in China? in Japan? in Saudi Arabia? in France? in a city? in a rural town?
Do you believe your results would change, and if so, how?

Questions that invoke a wider subject-matter:

Your findings suggest X; what does X imply about Y policy?
How should we think of X in terms of educating children/organizing airports/work-life balance/political advertisements/the effect of social media on young people/the effect of social media on middle-aged Millennials?

These two additional types of questions are also usually appropriate, though they probably appeal to a smaller subset of the audience than the above questions.

Questions that invoke a question-asker's motivated interests:

Your findings suggest X; I study A: how should we take your findings into account for A?
Note: Whether you think these are "good questions" probably depends on your motivated interests
Your findings suggest X; I study Africa. Africa will have the majority of the world's younger population by 2050: how can we use your X findings to support the growing young populations of Africa?
Your findings suggest X; My uncle is a farmer/trucker/plumber/construction worker and is concerned about how he's going to feed his family: what kinds of policies do you X findings imply about the future of my uncle's livelihood?

Goof-questions:

Your findings suggest X; how can I convince my mother-in-law that X is true?
Note: I don't like these, but some people like humorous questions if the question is very brief.
Ideally, a goof-question like this does have an element of usefulness or truth to it. In the present example, the underlying useful question is, "How would I explain this to a layperson?", which is itself a reasonable question.

Info

The above examples largely came from abstracting the questions in the Q&A part of this panel, which I thought were pretty great questions, for the most part.

Questions that you might not want to ask

First off, definitely do not as "questions" that are "more of a comment than a question".
The Q&A period is not your time to comment to the audience. If you want to comment, find the speaker after the talk and start a conversation directly with them. Refrain from voicing your "comment" to an audience of people that aren't here to listen to you.

Tip

When it doubt, if you aren't sure of your question, bring it to the speaker after, once they've come off the stage and are milling about the conference. This lowers the pressure and can be a great way to make a one-on-one connection.

I haven't always been a great question-asker.
I have made mistakes, which I hope you can learn from. The situations that have caused me the most trouble are the following:

In case (1), I know I don't understand something, but I can't figure out how to turn that confusion into a question.
There isn't really anything to be done about (1). You keep paying attention and hope someone else asks in a way that answers what you care about or clarifies something for you. Case (1) can also happen if you show up to a talk later and missed some key information. Rather than try to ask a question, you might approach the speaker afterwards and ask if they could elaborate on the topic of confusion. That might spark something and it is a great way to start a conversation at a conference.

In case (2), there are two options: ask it because you want to raise attention to this issue (but you will look confrontational) or hold your question and talk to the speaker afterwards.
You have to learn to pick your battles on this one. Sometimes, to save face, you just hope that everyone else in the audience noticed what you noticed and won't take the work seriously. Sometimes, you're okay looking confrontational because someone is spreading misinformation and you feel the need to say your piece.

Personally, I think it is generally wiser not to ask in case (2) unless you know something seriously flawed and other people in the audience don't seem to notice (e.g. you hear people talking about how good the study is, but you know there is a major flaw). That said, case (2) are often my favourite questions to hear from others and they are sometimes important to ask. I know from experience that case (2) questions take a lot of courage to ask and the person asking them is often voicing what I wish someone would say. My ideal of science includes respectful critical peer review, not pretending that everything is fine. However, I understand that I am less averse to social conflict than most. It is important to remember the main purpose of conferences is to meet people and to network, not to make enemies by launching harsh public criticism. As such, if you see methodological flaws, consider bringing them up to the speaker afterwards, a little more privately.

In case (3) I'm not trying to be an asshole, but the question ends up putting the speaker on the spot. This is a lighter version of case (2).
I think of case (3) as an "Emperor has no clothes" question. In the story of the Emperor, adults are pretending to see clothing on the Emperor because they have been told that his new clothing has been made of magnificent cloth that appears invisible to incompetent people; not wanting to seem incompetent, they go along with the situation, ignoring that they cannot see the clothing. Finally, a child innocently points out that the Emperor is naked in the street. The child means no harm, but their honesty causes great distress. In case (3), I play the part of the child.

Example

For example, a fellow graduate student in my department gave a presentation about "ego depletion".

"Ego depletion" isn't my area of expertise. I didn't know the literature on the topic. Naive as I was, I asked a question along the lines of, "how do you define ego depletion and how does it differ from general fatigue?" To me, this question was totally innocent: I was just trying to understand the research.

As it turned out, this question put the speaker in a spot: they weren't able to coherently answer the question. Their face turned red and they must have been nervous because they basically fell apart. It was awkward for everyone.

It wasn't my intention to pick on them or stump them with a trick-question; I innocently thought it was a reasonable question. I later heard through the grape-vine that they complained about me to some of their lab-mates. My question made me look unsupportive and I ended up looking like an asshole without trying.

How should we handle case (3)?
Honestly, I am not totally sure. To this day, I naively think my question was reasonable. I'm not sure how I could have known, in advance, that I shouldn't ask it. Similarly, I'm not sure how anyone else could guess that they are in case (3) beforehand. However, if you suspect that you are, as above, it might make more sense to bring the question directly to the speaker after the presentation is over. That will give them a chance to answer it in a lower-stakes setting (rather than on-stage, in front of an audience).

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