Joel on Software gives a lot of good advice on having a good customer service. You should listen to what your customers (or users) say. Don't dismiss them. Don't give them annoying canned responses. Open your bug-tracker to the world as a web-service. There are many web-based, and gratis bug-trackers, such as Bugzilla, and you should use one of them for better interaction with your customers.
As Joel indicates, a bug report, email, or query usually indicates a problem in the software: a bug, a missing feature, or something that's not clear enough. Such problems need to be fixed in the code.
Furthermore, if one or more of your customers are requesting a feature, and it seems to be important enough, give a priority to implementing it. As a Mercury Interactive (Now part of HP) developer noted usually the features requested by the customers, are the ones that will yield the most newer customers, not-to-mention will allow keeping customers, if they are paying for upgrades or as a "software-as-a-service" model.
Joel Spolsky also notes that good customer service is part of the key to a small ISV's success.