Theorem: It is undecidable in general whether an automorphism is inner.
Proof: To see this, note that every group is the outer automorphism group of some group. Therefore, we can take some group $G$ such that $\operatorname{Out}(G)$ has insoluble word problem. In this group it is undecidable whether an automorphism $\alpha$ is in the kernel of the map $\operatorname{Aut}(G)\rightarrow\operatorname{Out}(G)$. This kernel is precisely the inner automorphisms, and so we are done.
Comment: We used the result that every group is the outer automorphism group of some group. See, for example, the paper of Bumagin-Wise entitled Every group is the outer automorphism group of a finitely generated group. Download it from Wise's website here (it is under "Every group is an outer automorphism group"). However, the Bumagin-Wise result does not give you a group $G$ which is finitely presentable (apart from in certain exceptional circumstances which are not applicable here). To see that there are finitely presented groups whose outer automorphism groups have insoluble word problem, begin by taking $A_0$ to be finitely presented with insoluble word problem and take $A:=A_0\ast \mathbb{Z}$. Then form $H=A\ast B$ where $B$ is finitely presented and non-trivial, and take the automorphism $\tau_a$ defined by $\tau_a(x)=a^{-1}xa$ for all $x\in A$ and $\tau_a(y)=y$ for all $y\in B$. Then $\tau_a$ is inner if and only if $a\in Z(A)$, but $Z(A)$ is trivial by construction. Thus, $\operatorname{Out}(H)$ has insoluble word problem, and the result is proven. This construction is due to Arzhantseva, Lafont and Minasyan.
Anyway, the following result is related to the theorem. I quite like it.
Lemma: It is undecidable in general whether two (inner) automorphisms define the same automorphism of the group.
Proof: To see this, take $G=H\ast\mathbb{Z}$ where $H$ has undecidable word problem (so $G$ has undecidable word problem and trivial centre). Write $\gamma_g$ and $\gamma_h$ for the inner automorphisms of $G$ corresponding to $g$ and $h$ respectively. Then $\gamma_g=\gamma_h$ if and only if $gh^{-1}=1$, which is undecidable as $G$ has undecidable word problem.