There are some good suggestions in the post and in the comments, especially by David Barrett of Expensify and Lance Walley. Two suggestions I would add:
o probe for how satisfied customers would encourage others to try your product.
o listen to "drop-outs" to understand what is dissatisfying
Here are two blog posts that contain more suggestions for direct conversation to understand customer perspective from the stories they tell you as much as the multiple choice questions they answer.
The Best Feedback From Your Early Customers Is a Story http://www.skmurphy.com/blog/2007/11/29/the-best-feedback-fr...
The Best Way To Get Feedback From Early Customers Is a Conversation http://www.skmurphy.com/blog/2007/11/28/the-best-way-to-get-...
EDIT: It's also good to bear in mind http://xkcd.com/523/ for the limits of numbers for understanding relationships, Lord Kelvin's injunction to "measure everything" doesn't always lead to greater understanding.