A couple of other things I forgot to mention, when downloading several files at once they become incredibly fragmented across your harddrive so I sugguest regular defrag, before Limewire I use to defrag once a month, now its once a week if not more.

Last thing I can think of at the moment, check that your primary harddrives DMA is turned on, for some reason it gets turned off occasionly on my computer and this increases cpu usage because it now has to transfer between memory and harddrive instead of direct memory access between the drive and memory.