Synthetic elaboration of self-assembled monolayers (SAMs) provides a powerful method for the preparation of smooth, ordered surfaces with carefully controlled functionality. Chemically rugged siloxane-based SAMs have been employed as a foundation for the preparation of a variety of functionalized surfaces. Nucleophilic displacements are described between halide-terminated SAMs and anionic nucleophiles (e.g. azide, thiocyanate, thiolate). Problems were encountered due to the steric congestion surrounding the terminal bromomethylene carbon. The concept of trajectory control is applied to these displacement reactions. In addition, reactions between ester-terminated SAMs and neutral nucleophiles (e.g. amines, hydrazine, hydroxylamine) are described. Evidence is presented suggesting that a modest amount of cross-linking (i.e. imide formation) takes place in the amidation reactions, while reaction stoichiometry indicates that cross-linking is virtually complete for the bifunctional nucleophiles. These synthetic elaborations were also carried out on mixed monolayers to create functionalized SAMs with systematically varied loading densities. Linear correlation (or lack thereof) of elemental composition to predicted functional composition is used to provide an estimation of reaction efficiency.