PWM doesn't work with my sketch
One omission from your code which might be causing the problems is the fact that you haven't set the pinMode. You need to set the pins as OUTPUT in setup() 

#efine FAN1 3
#define FAN2 5

void setup() {
    pinMode(FAN1, OUTPUT);
    pinMode(FAN2, OUTPUT);
}

void loop() {
  int speed1 = 127;
  int speed2 = 25;
  analogWrite(FAN1, speed1);
  analogWrite(FAN2, speed2);
  delay(10000);
}


I am curious to know why you declared FAN1 and FAN2, but didn't use them - I'd recommend changing the analogWrite statements to use them instead of referring to the pin numbers directly.

Also, the way you're using the pin and speed means that you're using speed2 for FAN1 and vice versa, I've switched these in my example so FAN1 and speed1 go together.