I see no reason to lock this thread...
I find CPU usage goes pretty high when sync game to audio is turned on when using jabo's audio plugin -- which is probably done by design. You might consider looking around for another audio plugin if this is the problem...
If its not audio related then I'd go with what the others are saying... make sure fps limiter is on. Also double check your video plugin configuration and make sure its using the defaults. Well, that actually goes for everything... try and make sure PJ64 is running on its default settings, if you find memory usage and cpu usage stabilizes then either you modified something you "werent supposed to" or something got messed up (it happens).
Other than that, make sure your system is bug free (no virus, malware, adware, spyware, etc...), is loaded with the latest drivers (or what people recommend on these boards) and well... Keep us informed... We might not be able to help but we'll try. Well I cant really think of anything else, If I do I'll come by again... sometime
Oh yea, it helps to posts your computer's full specs, sometimes we can spot a problem just by looking at the specs.