How to launch local system application from Remote Desktop Application (Windows 2008R2)

Sounds like you need Terminal Services Remote Apps, which is in Server 2008. As the technet blurb says:

With Terminal Services, organizations can provide access to Windows®-based programs from almost any location to almost any computing device. Terminal Services in Windows Server® 2008 includes Terminal Services RemoteApp (TS RemoteApp). You can use several different methods to deploy RemoteApp programs, such as Terminal Services Web Access (TS Web Access). With TS Web Access, you can provide access to RemoteApp programs through a Web page over the Internet or over an intranet. TS Web Access is also included in Windows Server 2008

Im not sure if a web interface is good enough for what you need, or if your looking for something more integrated. See here for details on TS Remote Apps and here for details on how to do it.

You can achieve a better integration between applications running on a terminal server and those running on the local system usign Windows 2008 Terminal Services (RemoteApp); but a remote session is completely isolated with Windows Server 2003, apart from clipboard sharing.