It's possible to crack a program running in a virtual machine (VM) or is there any difference between the local system and a vm (like vmware, virtualbox...)?

1) yes
2) there are lot of differences between the physical system and virtual system but they do not come into play when dealing with simple user-mode applications
those differences and their consequences are visible only when dealing with kernel stuff

regarding the differencies between VM and real systems, there are many tricks used by viruses and protection programs; as usual, Google is your friend...
have a look for example at this thread:

http://reverseengineering.stackexchange.com/questions/1686/how-to-detect-a-virtualized-environment

Best regards
bilbo