debug.js

require.extensions['.js'] = function(module,filename) {
	var content;
	content = require('fs').readFileSync(filename, 'utf8');
	return module._compile(content.replace(/^ *\/\/debug: */gm, ''), filename);
}

file.js

//debug: console.log('This will be printed in debug mode only');

server.js

var options = {debug: true}

if(options.debug) require('./debug.js');

require('./file.js');

while(1) {
}