After putting the bones of a ghost into a hole I was shocked with a 25 Karma gain. What can I do with it? What does Karma even mean in this game? Unfortunately, I saved and now I am stuck with it.

So you are going for an evil character? I can try to explain it but wiki might do it better: http://fallout.wikia.com/wiki/Karma Pretty much it effects how people see you.

You can just go around killing non hostile civilians in random encounters to lose karma (bootleggers, caravans, farmers, etc...)

Do good - gain karma - good character that good people like
Do evil - lose karma - evil character that good people dislike

Walking the path of evil is not always easy in comparison to good or neutral.

Check this evil walkthrough for all your evil deeds: http://www.neoseeker.com/resourcelink.html?rlid=23897&rid=22674

Destroy the Gecko Nuclear Reactor, see you karma going to Oblivion literally