I am having this issue too.
I'm using the cpu-mem applet too, and I'm getting CPU spikes CONSTANTLY.
Switching through apps are painfully slow a lot of the time, since the N900 sometimes won't react to my input at all, sometimes it'll react 3-4 seconds after I've pressed.
And when it finally decides to switch to another windows, the drawing of the window is also extremely slow and choppy.

Music playing in the background will randomly skip, when multitasking are opening a new link in the browser. Again because of the CPU spikes.

Receiving a phone call while I'm listening to music, and browsing mobile websites, is always a gamble, since I won't know if I can answer in time.

I've tried running conky, but every time I get the cpu spikes, I can't multitask and switch to it, hence, I can never get to see exactly what is causing these spikes. I can see, however, that the cpu is toggling up and down constantly. Seems excessive for light use.
Is there another system load app, that will survey the cpu use, and output it to a log, for later investigation ?