There's a huge thing that's has not been mentioned here.
I talked to the developer's of Disk Warrior last year at MacWorld. They said that there #1 friend is Limewire due to the amount of directory damage it causes. They've found Limewire to produce an overwhelming amount of what they called "Overlapping Files" which in turn cause directory damage.
I to have come to the conclusion that this is 100% true. I've fixed probably 1000 mac's with the typical boots to gray apple spinning gear, or boots to gray screen or boots to blue screen. Boot to an external HD and run disk utility to find red file corruption all over. I then ask if they run limewire, and I'd say a good 75% of the user would say yes.
Limewire is very good at causing directory damage. I recommend using anything but it. I use aquisition and the ever so good xtorrent.