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The SR-71 had an automated celestial navigation system that could get a lock in daylight: http://en.wikipedia.org/wiki/Lockheed_SR-71_Blackbird#Astro-...

(The big disadvantage is that it can't see through clouds, of course)

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Didn't it fly above the clouds?

It was a surveillance aircraft, so it would need line of sight with the ground as well, which might require flying under cloud cover. Also, having a gyroscope component, I'm guessing that it would need to calibrate while stationary, on the runway.

It didn't fly under cloud cover. It flew Mach 3.3, which it couldn't do in dense air. Also, flying at 80,000 feet makes it much more difficult to shoot down.

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