When you enter a call in OS X, as of Mavericks, it lowers the volume of everything else besides the call. There's no way to disable this “feature.”
Solution: Before making the call in the application, paste one of the following line into terminal.
printf "p *(char*)(void(*)())AudioDeviceDuck=0xc3\nq" | lldb -n FaceTime printf "p *(char*)(void(*)())AudioDeviceDuck=0xc3\nq" | lldb -n QQ printf "p *(char*)(void(*)())AudioDeviceDuck=0xc3\nq" | lldb -n Skype