Will there be perks that are earned through gameplay, or only perks that you choose when you level up? For example, in Fallout: New Vegas you'd get a small perk for using stimpacks enough times. Anything like that in Skyrim?

The closest thing to this that I know about, are the Magical Sign stones placed randomly throughout the world, they give perk-like constant affect abilities. In a demo that I saw, The warrior stone gives your combat skills the ability to increase faster. However, you can only have one of these stones activated at a time.

As for extra non-skill specific perks, I haven't heard anything, but I think that it would be cool.

I really hope so. The little perks, like +3% damage vs. insects or whatever, were nice rewards, made you feel like you were getting somewhere, and didn't make a mockery of the difficulty.
Or some like Moira's perks in FO3. I noticed in Vixulation's thread, a mention of a quest for the Bards. Do a quest or two for them, get a small speechcraft perk or something, that would be wonderful, and also appeases those who prefer exp. over learn as you do, as the former gives character progression rewards for quest completion, the latter only cash or equipment.

I'm not sure how it would be making a mockery of anything. ? I think in order to get to that particular perk (like destruction), you have to use your destruction skill. I don't see them allowing you to put points in areas you don't use, so...it's the same thing in the end.