Quaternions came up while I was interning not too long ago and it seemed like no one really know how they worked. While eventually certain people were tracked down and were able to help with the issue, it piqued my interest in quaternions.
After reading many articles and a couple books on them, I began to know the formulas associated with them, but still have no clue how they work (why they allow rotations in 3D space to be specific). I back-tracked a little bit and looked at normal complex numbers with just one imaginary component and asked myself if I even understood how they allow rotations in 2D space. After a couple awesome moments of understanding, I understood it for imaginary numbers, but I'm still having trouble extending the thoughts to quaternions.
How can someone intuitively think about quaternions and how they allow for rotations in 3D space?
Here's one way. The group of unit quaternions is isomorphic to the special unitary group $\text{SU}(2)$, the group of $2 \times 2$ unitary complex matrices with determinant $1$. This group acts on $\mathbb{C}^2$ in the obvious way, and so it also acts on lines in $\mathbb{C}^2$. (These are complex lines, so they have real dimension $2$.) The space of lines in $\mathbb{C}^2$ is the complex projective line $\mathbb{CP}^1$, and it turns out there is a natural way to think about this space as a sphere - namely, the Riemann sphere. There is a beautiful projection which is pictured at the Wikipedia article which shows this; essentially one thinks of $\mathbb{CP}^1$ as $\mathbb{C}$ plus a "point at infinity" and then projects the latter onto the former in a way which misses one point.
So $\text{SU}(2)$ naturally acts on a sphere, and as it turns out it naturally acts by rotations. This describes the famous 2-to-1 map $\text{SU}(2) \to \text{SO}(3)$ which allows quaternions to describe 3D rotations.