As you said, "ga" is used to indicate specific things, and in some cases can serve as a topic marker. In the first two examples your topic is being marked by "wa". In the case of the latter three examples, the topic.
The first example asks "When is the meeting?".
Kaigi (meeting)
wa (topic marker)
itsu (when, question word)
desu (copula, in this case "is")
ka (question marker)
In this example you are talking about when the meeting is, and "when" is serving more as a property of the meeting.
An example of what I mean is "Watashi wa juu ni ji ni kaigi ni ikimasu.", translated as "I will go to the meeting at 12 o'clock."
In this case the first "ni" marks the specific time, "12 o'clock", and the second "ni" indicates the location I will be going to ("ikimasu" being the -masu form of iku, or "to go"). "Wa" marks the topic, myself.
The question form would be "Watashi wa itsu kaigi ni ikimasu ka?", which asks "When will I go to the meeting?". The topic is still myself, and in this case you do not need a "ni" particle for the time ("when"), though you still need to mark your destination ("kaigi") with a "ni" particle.
Going back to the example, an answer to the question would be "Kaigi wa juu ni ji han desu.", or "The meeting is at 12:30."
In this case there is no particle marking the time because the topic is the meeting, and the time serves as a description of the meeting (being marked/followed by "desu"). It would be wrong in the question form to say "itsu ga", because "when", as I said, is serving as a description of the topic, not as the topic itself.
The second example follows a similar pattern. An answer to "Kore wa nan desu ka?" would be "Kore wa pen desu." or "This is a pen." "Kore" ("this") is the topic and "pen" is describing it. "Kore wa nan ga desu ka?" would also be wrong because again, "kore" is the topic, and "nan" is a description of the topic.
The last three examples you provided however are different, specifically in that the question word is the topic.
The third example asks "Who is in this room?". As you saw in my example of when I will be going to the meeting, the location "kono heya" is marked with "ni", since it is the location of the topic "dare". "imasu ka?" is asking "what animate/living object is at the location?" In an example answer sentence, "Kono heya ni sensei ga imasu.", would say that "the teacher" or "our teacher" (remember, context can be crucial for small nuances in any language), is in "this room". In this case, "wa" is not used since the topic is followed by "imasu" (-masu form of "iru").
The fourth example is asking "What is in this room?", and is just two words different than the third. "Nani" is "what", and "arimasu" (-masu form of "aru") is basically the same thing as "imasu", except it is used for inanimate/non-living objects. You wouldn't say "dare ga arimasu ka?" instead of "dare ga imasu ka?", just like you wouldn't say "what is there?" instead of "who is there?" in English.
Another ordering with (I think, someone correct me if I'm wrong:) the same exact meaning, would be "Dare ga kono heya ni imasu ka?" and "Nani ga kono heya ni arimasu ka?".
The fifth example asks "Which is your book?"
"Dore", which
"ga", marking the topic, asking specifically which item it is
"anata no", your
"hon", book
"desu", copula
"ka", question marker
Again, "your book" is describing the topic, which in this case happens to be unknown. An answer would be "Kore ga watashi no hon desu." or "This is my book.", and this is where the extended meaning comes in. When you say "ga" in the answer here you are saying "this is my book" and are implying "and only this book is my book". If you say "Kore wa watashi no hon desu." you are saying still that the book you are indicating/holding is "my book", but you are not saying that for sure that is the only book that is yours. Using "ga" would be like emphasizing "This" in "This is my book.", or saying "This, and only this book, is my book." Using "wa" would be like saying "This is my book [but so is that one that you're holding, and that one over there]." (<- implication in []'s).
To put it simply, "wa" and "ga" can both serve as topic markers, with "ga" being more explicit and specific. In addition, when the topic is also the "unknown" part of your question, you need "ga" because you're asking specifically for an answer.
To my knowledge you can't, or it would be extremely unnatural to say for example "Dore wa anata no hon desu ka?" (if I'm wrong/not completely right can somebody more experienced correct me?), and I can't think of any example where the topic would be unknown that you would not use "ga" to indicate it. As I said earlier, in the first two examples the unknown "variable" so to speak in the sentence is not the topic, but something that describes the topic, and is therefore not marked with "ga".
An example of where you would use "itsu ga":
"Itsu ga ii desu ka?", in English "When [specifically] is a good time [for you]?", or colloquially "When is a good time?".
"Nan" and "nani" are both what and indicated by the same kanji "何{なに｝", so your fourth example already covers an example of where "何が{なにが｝" would be used (I cannot however, thing of a place where you would say "nan ga" instead of "nani ga"), but as another example of where "何が{なにが｝" would be used is "Nani ga John-san no suki na tabemono desu ka?", which is in English. "What is John's favorite food?".
"Nani ga", what specifically is
"John-san no", John's
"suki na", literally "liked", colloquially in English we would say "favorite"
"tabemono", food
"desu", copula
"ka", question marker
I hoped this answered your question. If my answer didn't clear up your confusion please comment so I can improve my answer for you.
