I think most such implications come from the nature of the question.
If I ask, "Is Sally telling the truth?", the fact that I'm asking the question implies that I think she may not be. We don't normally ask if what someone says is true, normally we just assume that what people tell us is true, so if you ask, you're implying that you doubt it.
If I ask, "Is tomorrow Christmas?", I suppose that as Christmas comes only once a year, the question implies that I think it is. Though in that case, I think the implication would depend a lot on the context. Like, "Of course the office will be closed tomorrow." "Oh, is tomorrow Christmas?" In that case I'd think the person had lost track of the date, but now that he's been told that the office will be closed he is expecting a yes answer. But, "The boss said he's getting us all new computers tomorrow." "What, is tomorrow Christmas or something?" Here I'd assume the real and expected answer is no.
There are plenty of times you could ask a question like that with no implication. Like if someone asked, "Is tomorrow a company holiday?", he probably genuinely doesn't know and neither a yes nor a no would be a surprise.
In the extreme case, there are "rhetorical questions", questions that are asked with a clear implication that the questioner already knows the answer. Like, "Don't you think my new girlfriend is beautiful?", or "Are you an idiot?" In either case, the questioner has already decided on the answer. The purpose of the question is not to gain information. In the first case he expects you to express agreement with the conclusion that he has already reached. In the second he is simply insulting you, and he might just as well have said, "You are an idiot." You know that that's what he meant.