Building a standalone application is largely the same as building a collective. You'll use the collective editor window to script the inclusion of files needed by the standalone. At the very last step, when saving, you choose Application as the type of file you want to create instead of Collective.

A collective file is built as part of the standalone process. As part of the application, it contains the contents of the init folder inside the Cycling '74 folder. This permits the standalone to start up properly. Once the collective is built, Max searches for the most recently created version of the Max/MSP Runtime application in the same folder as the Max application. It makes a copy of the runtime application, then combines it with the standalone. The exact details of this process and the format of standalone applications differs between the Mac and Windows platforms. Note that even though your original patcher file might be platform-independent, standalone applications created with Max are definitely platform-specific.