Geosyncline theory:
http://en.wikipedia.org/wiki/Geosyncline
This is a biggie; in the space of 10 years, the fundamental principles of Geology were completely overturned, and replaced with a new, unifying concept that explained nearly everything: Plate Tectonics. (It was like the French Revolution, except noone died and it actually worked.)
Also:
* The origin of the Moon's craters: Before the mid-1960's everyone thought they were volcanic, probably maars. Then, we started to get good telescopic pictures...
* The origin of the Moon itself: Before the Apollo samples were returned, most scientists thought the Earth and Moon formed together. Now, most think that it was formed via a Mars-sized impactor:
http://en.wikipedia.org/wiki/Giant_impact_hypothesis
* Static universe: Edwin Hubble's doppler measurements of galaxies was the first indication that the universe was not static, and indeed had a starting point...
* Uniqueness of the Sun: Before the invention of the IR telescope, the Sun was regarded as a smallish star, relatively speaking. Now, we know that the vast majority of stars are smaller than the Sun, and that the most common mass is 0.1 Msun...
And so on and so forth...
Simon