Mostly I hear five variations on this "noise".
"uh-huh", which is generally taken to mean "yes", or a doubtful acquiesence.
"nuh-uh", which is generally taken to mean no.
"err-uh", which is usually a pause to let the brain catch up with the mouth 
"uh-oh", which signifies that the speaker has made a mistake, or sportted a mistake that someone else has made, or is about to get into trouble over something.
"uh-uh!", which is a more emphatic negative, often employed when speaking to children or pets. If you see a child reaching for something they are not allowed to have, for example, or a pet attempting to eat something off the floor.
As for where they came from ... no idea. I suppose they are space-filling noises, whose spelling and accepted meanings are arrived at by consensus.
For example, I’m pretty sure that animals make pretty much the same noise wherever they are. In English, we say that a dog says "woof woof". In French, they say "oua oua!", in Japanese "wan wan!", in Italian "bau bau", in German "wau wau". A cat says "meow" in English, "miaou" in French, "nyan nyan" in Japanese.
The noise is the same, but our consensus on how to represent that noise is dependent on how our ears are refined toward hearing it.
In the same way, an Aussie represents "uh-huh" like that because (a) that’s how he hears it, and (b) that’s the consensus way of representing that noise. In American novels and scripts I’ve seen it written "uh-hunh". To my ear, there is no "n" in it. But to an American ear, clearly there is.
Azh
(who has overheard one end of a phone conversation that went like this: "uh-huh. uh-uh. er-uh. umm. uh-oh. uh-uh." <click>)