I think using nice or renice is better practice. Hard throttling is way more inefficient.
The bizarre part, when it comes to Flash, is that I've yet to see an actual difference in the application behavior when I throttle down it's CPU usage. I would think that if it normally maxes out 7 of my 8 logical cores, being limited to 40% of one core would make introduce slowness. But I guess that's just an indication of how poorly written the OS X flash client it.
I use cpulimit to force a CPU bound program to slow down. I also use it for programs that always max out the CPU for no good reason, and work fine with less CPU.
Nice won't help with either of those.