Opals are photonic structures with applications varying from coatings and pigments to photonics and optical devices. Colloidal self-assembly of polymer-based nanoparticles is a cheap and green method to create opals over large areas: recently, procedures combining co-deposition of crosslinker precursors and other additives with nanoparticle self-assembly have emerged as routes to large-area efficient deposition. We investigate how the presence of some common organic dyes and pigments affects the properties and self assembling behavior of core shell polystyrene particles with a poly(methacrylic acid) shell during horizontal deposition (casting) from water, studying both the variation of particles properties in solution and the structure and properties of the resulting films. The study further includes the effects of a precursor of silica crosslinking (Tetraethoxysilane), and its combination with the same dyes, and we are able to show how interactions starting in the nanoparticles dispersion affect the structure and properties of the crystals.