as others have said, the middle pickup on its own is really nice for clean or mostly-clean rhythm. its also nice for the quacky sounds when combined with the bridge or neck.
in my opinion though when you load on some gain, to harder rock levels, then the middle pickup loses some of its relevance. Its harder to distinguish its special tone from the neck pickup and those cool quacky tones aren't quite so useful. it depends on the rig though, since some people use the middle in a hard rock context. but certainly for me, i rarely use it.
also, if you drop the middle pickup from the wiring, you can very easily setup the bridge and neck together, which I think sounds absolutely amazing on a strat. i know theres various ways to get that combination, but without a middle pickup you just need a three way switch.