Working on this recent MSE question, I was led to the following conjecture :
Suppose that $n$ is an integer with at least one prime divisor $\geq 7$. Then $\Phi_n$ has at least seven non-zero coefficients.
I have checked this conjecture up to $n\leq 10^5$. It is not hard to treat the case when $n$ is of the form $p^a$ with $p\geq 7$. In the general case $n$ will be of the form $n=p^a m$ with $m$ coprime to $p$, and $\Phi_n=\Phi_{p^{a}}\Phi_m$. What is unclear to me is how non-zero coefficients are somewhat "preserved" when we multiply by $\Phi_m$ where $m$ is coprime to $p$.
UPDATE (10/18/2014) : One can assume without loss of generality that $n$ is square-free. Indeed, let $n=\prod_{k=1}^r {p_k}^{a_k}$ be the prime factorization of $n$, with prime $p_k$ and $a_k\geq 1$. Let $m=\prod_{k=1}^r p_k$ be the square-free part of $n$. If $\zeta$ is a $n$-th root of unity, then it is a primitive $n$-th root of unity iff $\zeta^\frac{n}{m}$ is a primitive $m$-th root of unity. It follows that $\Phi_{n}(X)=\Phi_{m}(X^\frac{n}{m})$, so that $\Phi_n$ and $\Phi_m$ share the same number of non-zero coefficients.