system-monitor
I've seen this behavior in MacOS's Activity Monitor as well.
An example: Playing Minecraft with OpenJDK. I frequently see over 100 CPU when the game's abusing the system. My girlfriend's MacOS has reported over 100 percent as well on her own programs (not just minecraft).
'nice' refers to the priority the process gets on your CPU. This is a number in the range of -20 (highest priority) to 19 (lowest). You'll probably find that most applications you're running are at nice '0', which means that they are running with normal priority and none will get preferential treatment by the scheduler over another.
If you're running an intensive program, you may wish to launch it from a terminal with nice -n 10 /path/to/program. That way it will impact less on the performance of your system.
Note that you need root (sudo) privileges to schedule a process with priority greater than normal (<0). This is to prevent users from being able to bog down the entire system easily, and so that critical tasks can always receive the CPU time they require.
There's a good explanation on Wikipedia too.
As suggested by Cedric Julien in the comments,
To view all the processes that are using CPU, when using System Monitor, go to the View menu and select All Processes
Best Answer
100% CPU usage represents full usage of one CPU core.
Anything above 100% represents a multithreaded process utilizing more than one core.