I doubt it makes much of a noticeable difference which slot you put usb, sound, and other cards. But from what I remember while researching the issue a while back, you should always put your gfx-card in "Slot 1". IIRC, this is literally to do with the bus-track's physical distances from the CPU. Shorter distance between the card and CPU = faster data transfer.
I'm no electronic engineer, so maybe someone else can give you the actual reasoning behind it, but I definitely remember being advised by more knowledgeable people to always put your gfx-card in slot 1 - if possible.
