I rarely bother to "rate limit" the amount of CPU my Linux processes can do, but since I unfortunately have to share my desktop with some CPU intensive tasks, sometimes it makes sense to do so, for multi-threaded applications at least. Linux has, for some time now, a feature to set CPU affinity for a process. This is btw something that Sun/Solaris have had for almost as long as I can remember. With this feature, you can specify which CPUs (cores) a process is allowed to use.
As an example, lets assume we want the application traffic_server to only consume core 2 and 3, you'd simply start the application with
# taskset -c 2,3 traffic_server
Now, some applications have this built in (unfortuantely traffic_server does not, yet), and there are APIs in linux to control this (see the man page for sched_setaffinity() ). You can of course also "nice" your application accordingly, but the above lets you get a somewhat more controlled behavior (again, for threaded apps that can use more than one core).