In a recent series of mass-spectrometric ion trap measurements [H. Hiura , Phys. Rev. Lett. 86, 1733 (2001)], the formation of silicon clusters with endohedral transition-metal impurities was observed. Particular stability was assigned to the experimentally detected species WSi12+, which has been shown by ab initio geometry optimization to adopt the shape of a regular hexagonal Si-12 prism with the W atom in the center. A similar geometry-namely, a Si-12 double-chair structure surrounding the metal atom impurity-has emerged from our extensive investigations of silicon clusters in combination with a Cu atom (CuSiN) as the likely ground-state structure of CuSi12. These results suggest the systematic importance of Si-12 cages derived from regular structures with D-6h geometry for the architecture of silicon clusters containing metal atom impurities. In the present comparative study, we discuss the salient features of endohedral MSi12 clusters with M=Cu, Mo, W, as well as several cationic and anionic species of these systems, with regard to their geometric and electronic structure. The interaction between the Si-12 cage and the enclosed metal impurity is characterized as strongly delocalized bonding for M=Mo, W, while Cu tends to form directed bonds with selected atoms of the cage. Linear extension of the MSi12 (Me=Mo,W) cells along their principal axes leads to units of the form M2Si18.