Before you even approach (or send a query letter to) an agent, you should do your homework. You should already know some of the authors the agent represents and what genres the agent feels most comfortable selling. For example, you wouldn't send a romance to an agent who mainly sells sci-fi.
You should also already know what percentage of your advances/sales/royalties the agent will take, usually 15% of books and 20% of movies/TV. Most guides to literary agents state this up front.
Because I did my homework, these are the only questions I asked my agent in 2000:
1) Where are you sending the manuscript first?
2) What is the best way to reach you? Email? Phone?
3) How do you prefer I send you my work? Email attachment? Snail mail manuscript?
I also asked, "Why did you choose me out of all the writers in the world?"
This is a business relationship, so keep your questions business-like.