AppLink is a great feature of ThinApp. The possibility to merge two or many packages together allows for a much more modular deployment model. But how do your deploy your AppLinks?
I think we (read VMware) did ourselves a big disservice when we decided to add ;OptionalAppLinks=plugins\*.exe as a default setting in the package.ini file. Many out there now think it is required to use a folder called plugins relative to the parent package in order to use AppLink. This is far from true.