I've only encountered that once or twice but one of the key things is...

If you're installing a ton of apps and not on 1.1 firmware yet, make sure to reboot/poweroff occasionally to clear the icon cache so you're not filling your rootfs.

Also, if you have a lot of files on your device it could be the tracker process indexing them.

Since you "just got your n900" doublecheck you're on the newest firmware. That's always the best place to start.