I've read over and over again that you're supposed to only send your query to five of your favorite agents at a time. Five out of hundreds... how do I make the choice?
The best way (as far as I know) is to query agents who represent books you like and are similar to yours. You can find out who represented a certain book by looking in the acknowledgments.
My other technique is to just keep my eyes and ears open. You should interact with the writing community as much as possible, and when you are involved, you pick things up.
For example, I'm interested in Donald Maass because I read How to Write a Breakout Novel and Career Novelist. I expect to be rejected because he doesn't represent books like mine, but I'm so impressed by his knowledge that he's made the top of my list.
I'll also send queries to all the agents who went to the Historical Novel Society Conference because I know they're passionate about historical fiction, not lukewarm.
There are other agents I'm interested in because clients of theirs have told me good things about them.
I don't think there's any perfect way to go about this, but I do believe just paying attention is the best way to find the right agent for me.