Wow great question. Check up's happen every time you lay hands on an animal.
Feel them move, is it normal ?
Check eyes, normal color and clarity?
Body in good shape, not to skinny not to fat?
Vent and nose clear of discharge?
More often than not people catch problems because they know what is normal physically and behaviorally for that animal. People that don't are the ones that open their tub one day to find their snake drooling and blowing bubbles, or not moving the lower half of its body (no reference to any user here just a general statement).

Knowing your animals is the key to everything from breeding to spotting health issues early.