Another approach: This is the same basic approach as in Peter's answer, but gets at the value in a different way. Let $m = $ the number of $1$'s in the binary expansion of $n$. Then the answer is $n-m$. Since the binary expansion of $100$ is $1100100$, the answer is $100-3 = 97$.
This can be seen as follows: As per Peter's answer, we are calculating $P_2$, the exponent of $2$, as
$$
P_2 = \sum_{k=1}^\infty \text{trunc} \left(\frac{n}{2^k}\right)
$$
Peter has it as $k = 1$ to $6$, but since the truncations after $k = 6$ add nothing, this doesn't change the final result, and will make the explanation clearer (I hope). On the other hand, we can also write
$$
n = \sum_{k=1}^\infty \frac{n}{2^k}
= \frac{n}{2} + \frac{n}{4} + \frac{n}{8} + \cdots
$$
If we write $n$ out in binary, we find that the difference $n-P_2$ is accounted for exactly by the $1$'s in that binary expansion: As we successively halve $n$, we have an excess whenever a $1$ is encountered in the ones digit. At that point, halving produces an excess of $1/2$. In the next halving, it produces an additional excess of $1/4$, then $1/8$, etc. As a result, as $k$ runs from $1$ to $\infty$, each $1$ produces an excess of $1/2+1/4+1/8+\cdots = 1$. The total excess is therefore $m$, and since $n-P_2 = m$, it follows that $P_2 = n-m$.
Just for good measure, the exponent of $2$ in prime factorization of $(100!)!$ is $100! - 207$, since there are $207$ $1$'s in the binary expansion of $100!$ (which has $525$ digits in all, the last $97$ of which are $0$, as you would expect).