I leave my desktop on and usually awake even if I'm not using it because I like it to be available for streaming media to my stereo. However, if I go out of town, I shut down and unplug it. I do have a good surge protector, but I figure if something did go haywire (lightning or otherwise) it's safest to have it totally disconnected.
Note that if you're worried about this you should unplug any Ethernet cables and connections to USB devices with separate power supplies (or unplug their power supplies too -- I just unplug my surge protector and that takes care of everything). Lightning can come in through your cable/DSL line and propagate to everything physically connected to your router; it can also come in through anything plugged into the wall. So think about your chain of devices and, if you're going to bother doing this in case of storms, extended absence, or whatnot, make sure you unplug everything in the chain.
Starting up is one of the biggest stresses you can put on your hard drive, so if you're concerned about longevity, shutting down, unplugging, plugging in, and restarting every day probably isn't the best idea. On the other hand, it's not so much of a stress that an *otherwise* healthy drive will fail because of this. It may bring existing problems to light more quickly, though.
