Receiving commands through Serial port

I will be sending commands with 2-3 parameters to Arduino, from Java program. Now problem is that frequency of these instructions might vary, from 10 a minute, to 1 per hour. Somehow Arduino needs to be always on the alert, but actually there will be only work to do, from time to time. What would be the best way to code this in Arduino? should I use NewSoftSerial library or should I just stick with standard Serial lib?

You probably want the standard Serial lib, since you'll be communicating via USB, which is connected to the default serial pins.

As for processing the serial input, try something like this:

void loop() {
  while (Serial.available()) {
    char c = Serial.read();
  }
}

This will only process the Serial input when something arrives - you can do other processing in the loop too.