Here is a list biased towards what is remarkable in the complex case. (To the potential peeved real manifold: I love you too.) By "complex" I mean holomorphic manifolds and holomorphic maps; by "real" I mean $\mathcal{C}^{\infty}$ manifolds and $\mathcal{C}^{\infty}$ maps.

• Consider a map $f$ between manifolds of equal dimension. In the complex case: if $f$ is injective then it is an isomorphism onto its image. In the real case, $x\mapsto x^3$ is not invertible.

• Consider a holomorphic $f: U-K \rightarrow \mathbb{C}$, where $U\subset \mathbb{C}^n$ is open and $K$ is a compact s.t. $U-K$ is connected. When $n\geq 2$, $f$ extends to $U$. This so-called Hartogs phenomenon has no counterpart in the real case.

• If a complex manifold is compact or is a bounded open subset of $\mathbb{C}^n$, then its group of automorphisms is a Lie group. In the smooth case it is always infinite dimensional.

• The space of sections of a vector bundle over a compact complex manifold is finite dimensional. In the real case it is always infinite dimensional.

• To expand on Charles Staats's excellent answer: few smooth atlases happen to be holomorphic, but even fewer diffeomorphisms happen to be holomorphic. Considering manifolds up to isomorphism, the net result is that many complex manifolds come in continuous families, whereas real manifolds rarely do (in dimension other than $4$: a compact topological manifold has at most finitely many smooth structures; $\mathbb{R}^n$ has exactly one).

On the theme of zero subsets (i.e., subsets defined locally by the vanishing of one or several functions):

• One equation always defines a codimension one subset in the complex case, but {$x_1^2+\dots+x_n^2=0$} is reduced to one point in $\mathbb{R}^n$.

• In the complex case, a zero subset isn't necessarily a submanifold, but is amenable to manifold theory by Hironaka desingularization. In the real case, any closed subset is a zero set.

• The image of a proper map between two complex manifolds is a zero subset, so isn't too bad by the previous point. Such a direct image is hard to deal with in the real case.