The processors and basic hardware have been mostly commodity since the mid 90s, the interconnects and related technology have mostly been specialized hardware though you could always do grid computing with Ethernet and the like.
True. Things like the Crays have their own, specialized interconnects and OS (on work nodes). A lot of things that aren't trying to be in the top can use fiber channel for similar results, though.
There isn't a terribly large difference anymore except for size and tuning.