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.