Use Google's Closure Compiler with WHITE_SPACE_ONLY and PRETTY_PRINT -- the only thing that it will do is remove the comments (Unless of course you don't format your code in the way that PRETTY_PRINT does.)
It turns this:
// This function alerts a name
function hello(name) {
/**
* One lone
* multi-line
* comment
*/
alert('Hello, ' + name);
}
hello('New user');
Into this:
function hello(name) {
alert("Hello, " + name)
}
hello("New user");