For example I would like to take this hack:

Countdown Timer for your users - vBulletin.org Forum

And replicate it multiple times. For example I want to a countdown number 1 and a countdown #2 and a countdown #3 but this hack only allows for one.

Any good solutions?

It's just a matter of tweaking the code to work with different field id's by the looks of things. That would be my guess but I havn't looked at the code.

Can anybody elaborate a bit on how this can happen in detail?

The author has disapeared I believe. It's not really something any honest coder could do publicly such as releasing it since it's Hellcat's code. But I'm sure you could find a good coder to customize it for your personal use.