1. The mountains are shaped like pegs:
Have We not made the earth as a wide expanse, And the mountains as pegs? (78:6-7)
Early tefsir made prior to scientific discoveries:
Tafsir.com Tafsir Ibn Kathir
Scientific article that confirms the shape of mountains:
Beneath the mountains
2. Mountins protecting us from earthquakes.
And We have set on the earth mountains standing firm, lest it should shake with them, and We have made therein broad highways (between mountains) for them to pass through: that they may receive Guidance. (21:31)
Early tefsir prior to the scientific discoveries:
http://www.tafsir.com/default.asp?sid=21&tid=32959
Article explaining how research confirms the function of mountains as insulators for earthquakes:
Effects of Large-Scale Surface Topography on Ground Motions, as Demonstrated by a Study of the San Gabriel Mountains, Los Angeles, California -- Ma et al. 97 (6): 2066 -- Bulletin of the Seismological Society of America
2. The deepness of the sea:
Or as darkness on a vast, abysmal sea. There covereth him a wave, above which is a wave, above which is a cloud. Layer upon layer of darkness. When he holdeth out his hand he scarce can see it. And he for whom Allah hath not appointed light, for him there is no light. (24:40)
Claims that:
1. Deep inside the sea there is darkness, this has now been tested with diving equipment and validated.
2. There are different waves above each other. This has now been tested with hightech equipment, measuring density and temperature, you can find "layers" of sea.
3. The darkness is caused by the layers. Again this is correct. These different layers of sea, since they each have a different density and temperature cause a phenomena which in science we call: "light refraction". Upon each refraction, a percentage of light is reflected back up. So the light is really stoped in part layer by layer.
(Do note this only acounts for part of the darkness, allot of the light is also reflected on the surface (+-30%) and also some part of it is "absorbed", nevertheless, that this verse does not contradict science is amazing)
Another: In Surah 'Alaq, its mentioned that man is created from an 'Alaq, which literally means something that hangs off something else.
And we know that the blood clot hangs off the womb to feed off the mother.