Question on wa and ga

Can anyone tell me what is the different between these 2 line:

好きな食物は何ですか?
好きな食物が何ですか?

How does が and は affect the sentence?
Please advice.
Thank you.

From a learners point of view:

ha refers to the topic as well as the subject, ga refers only to a subject.
So in the second sentence, the subject is not necessarily the main topic of the sentence and the sentence could be understood a bit differently depending on the context.

In general however, there is no different translation for the sentences in English, thats why so many people struggle that much with those two particles. :)

On a personal note, I wouldn't use the second sentence when asking someone what kind of foods they like, but that's just my personal preference.

Note that subject is not to be understood in the sense of a subject in english grammar, that's just what it's called. :)

Since I don't feel that I've giving any explanation whatsoever ^^, I recommend reading through the explanation by Tae Kim:
http://www.guidetojapanese.org/particles.html

As the previous poster says, the second sentence would not normally be used.

To illustrate the difference, let me try a couple of examples.

(1) 私は　行きます。
(2) 私が　行きます。

(1) would be an answer to the question, "What are you going to do?" or "Are you going or not?"
and
(2) would be an answer to the question "Who is going?"

So...
(1) is a plain "I am going" (while "I" have been the topic of the dialogue already)
and
(2) is like ""I" (with a big emphasis) am going" or "It's ME who is going," highlighting the subject "I".

Thus, "wa" is called the "topic marker" (it points to the topic of the sentence" and "ga" is the "subject marker."

Thanks for all the answers.
However, I still quite confuse. Maybe it is because my english is not very good either.
I think i just have to work harder in order to learn japanese well.

Regards,
JK