A method for linking a plurality of virtualized application packages for execution on a computer system is described. A runtime executable of a primary virtualized application package is launched. A secondary virtualized application package to be merged with the primary virtualized application package is identified. In one embodiment, application settings and file data for the first and second virtualized application packages are merged into a single data structure. An execution layer is created by starting execution of one of the application files associated with the primary virtualized application package. Requests from the execution layer to the operating system for configuration settings and contents of application files of either the primary virtualized application package or secondary virtualized application package and providing requested configuration settings are satisfied using configuration settings and file information from both the primary and secondary virtualized application packages.