The meanings in each pair are nearly identical.
over acknowledges an attempt to find a person or thing.
Without it, it can mean the same thing. But without it, there may
be more emphasis on arrival somewhere.
If I arrive at a party (to which I have been invited), I say "I'm
here!", not "I'm over here!" No one is trying to find me, of
course!
If I have strayed from the trail while hiking in the woods with
friends, and they notice I'm missing and call my name, I answer "I'm
over here!" to acknowledge the attempt to find me. (In this
situation, I can also answer "I'm here!";
over is not absolutely necessary.)
The penguins are there assumes the listener will see them
immediately. Or it may mean that the listener already knows where
they are. They are in the usual place where new penguins arrive,
and this statement just says that they have arrived. This can be
extended to
The penguins are there now. You can go and get them and put them in their new home.
The penguins are over there assumes the listener is trying to
find the penguins, most likely just visually as someone helps by
pointing, but also in the case where a zoo patron has just inquired
where the penguin exhibit is located, or even in the case of the
zoo-keeper whose penguins have got loose!
CJ