That happens to me. Less often than it used to but certain pipes w/ sharp bends or new and wet tobacco's will still get that gurgle. And yes if any gets in your mouth it's darn gross so spit it out!
I am fairly sure that most of that moisture is from the tobacco/smoke. As it burns and turns to smoke, the moisture in the baccy turns to water vapor, and sometimes builds up. If you run a pipe cleaner in there it'll normally catch most of it. Also, depending on the shape of the pipe, you can just lightly bat the mouthpiece into your palm and the moisture will fall out. So if you don't mind dirty hands and have some ruggy pants to wipe on, that works too.
In the end, drying your tobacco a bit before smoking, as well as smoking more slowly will both help to avoid moisture build up.