Given a polytopal complex $X$, we examine the topological complement of its $k$-skeleton. We construct a long exact sequence relating the homologies of the skeleton complements and links of faces in $X$, and using this long exact sequence, we obtain characterisations of Cohen-Macaulay and Leray complexes, stacked balls, and neighbourly spheres in terms of their skeleton complements. We also apply these results to CAT(0) cubical complexes, and find new similarities between such a complex and an associated simplicial complex, the crossing complex.