Bryce,
It depends on the "focus" of the sentence. For example, when we pose a question, we are saying, "OK, here is what we are talking about, and this is what I want to know about it."
For example, we can ask, "Tokyo wa doko desu ka?" Here, we mean, "OK, Tokyo is what we are talking about, and I want to know where it is."
Or, we can say, (Someone has already asked the question, "Doko e ikimashou ka?") "Tokyo ga ii desu ka?" Here, we mean, "OK, we are talking about where we want to go, and I want to know if Tokyo is a good choice."
Let's go back and look at the focus of both questions.
1) "Tokyo wa doko desu ka?"
2) "Tokyo ga ii desu ka?"
Our focus is on the words in italics -- after the wa, and before the ga.
Another way to identify the part being focused on is to break the listener's answer into a one-word repeat of the question (as if the listener did not hear the question, or is shocked by the question.)
1) "Eh? Doko...??!!"
2) "Eh? Tokyo...??!!"
This also explains why people translate "wa" as "as for."
"Tokyo wa doko desu ka?"
--> As for Tokyo, where is it?
The word "ga" cannot be translated in this way.
Now, let's use your sample of searching for a sake bottle.
1) "OK, now, which one of these bottle is that bottle of sake I saw yesterday?"
= "OK, that bottle of sake I saw yesterday is what we are talking about, and I want to know which one of these it is."
= "Kino mita sake bin wa dore desu ka?"
2) "Osake wa dou desu ka?" (The person is trying to choose whether they want to drink a bottle of sake, a bottle of beer, etc.)
= "OK, sake is what we are talking about, and I want to know if it sounds like a good choice."
= "Osake wa dou desu ka?"
3) "Osake ga hoshii desu ka?"
= "OK, we are talking about what you want, and I want to know if having sake sounds good."
= "Osake ga hoshii desu ka?"
Also, please think of "...ga hoshii..." as a set phrase. It almost always occurs in this form -- do not try to change this set phrase.