In the paper, combinatorial synthesis of structure for applied Web-based systems is described. The problem is considered as a combination of selected design alternatives for system parts/components into a resultant composite decision (i.e., system configuration design). The solving framework is based on Hierarchical Morphological Multicriteria Design (HMMD) approach: (i) multicriteria selection of alternatives for system parts, (ii) composing the selected alternatives into a resultant combination (while taking into account ordinal quality of the alternatives above and their compatibility). A lattice-based discrete space is used to evaluate (to integrate) quality of the resultant combinations (i.e., composite system decisions or system configurations). In addition, a simplified solving framework based on multicriteria multiple choice problem is considered. A multistage design process to obtain a system trajectory is described as well. The basic applied example is targeted to an applied Web-based system for a communication service provider. Two other applications are briefly described (corporate system and information system for academic application).