Some people, when asking a question at the end of a seminar, make comments on the talk first along the lines of "great talk," "really enjoyed this talk," or similar phrases. Is this a desirable thing to do? I've noticed that most people don't do this, but some of my favorite scientists do.
My personal preference is not to offer a compliment in this setting. It often strikes me as less sincere (off-handed or perfunctory). If I really want to compliment someone, I tend to catch up with them later and start with something like "I really enjoyed your talk. If you have a minute to talk, I have a question for you about..." On the other hand, I know that some people feel like asking questions (especially if they are critical of some aspect of the work) can feel hostile, and so they find the compliment as a good way to off-set that.
If it's your honest opinion, then I would compliment the talk. However, I wouldn't do it just to be polite. There is no need for false kindness.
When asking a question, it is desirable to explicitly establish a non-confrontational tone. It is natural and common (though of course not correct) to interpret even well-meaning questions in an antagonistic way. If the speaker feels threatened, they will be less able to focus on the content of the question and may instead become defensive. A question that is interpreted as non-confrontational is therefore likely to get a better answer.
Complimenting the speaker is one way to make your subsequent question non-confrontational, and is a good idea as long as you are sincere. Other ways include saying something nice about the topic itself ("you're studying a very interesting question"), smiling, and carefully controlling your tone of voice. These are especially important if your question amounts to a criticism of the presented material.
I agree with the other posters.
Personally, I try to make my tone of voice, attitude and choice of words respectful when asking a question while the conference is in session (and of course otherwise). I try to indicate indirectly that I enjoyed the talk (if indeed I did), without offering a direct compliment.
You note your favourite scientists being complimentary to speakers. I expect that these scientists are well-established, well-regarded and that they know that any praise from them would be a particular boost to, in particular, more junior scientists.
I think if you reason why you compliment the person, like "I really enjoyed your talk because [state your specific reason here]", it will always be warmly accepted.
It is not desirable, but you can do it if you want. But do it shortly, because there is not a lot of time for questions after a talk. Personally, I think that saving the compliment as a way to start a discussion later with the speaker is preferable.
To tell the truth, I also think that, except for clarification requests, questions are better asked in a discussion with the speaker, after the session. This is the only way to have complete and clear answers.
Somewhat like @Dan C suggested...
If you really felt inspired and got something new from the talk you should offer verbal appreciation. If you very much liked the presentation and is relevant to your research, it would be a good idea to talk in person.