Again a VBScript problem.
Here is a working code
Set WshShell = WScript.CreateObject(\"WScript.Shell\")
WshShell.Run \"\"\"C:\\Program Files\\TrueCrypt\
.Run starts a console ('DOS Box') to execute some other process/program. You can control the display mode of that console (e.g. hide it by passing SW_HIDE == 0 as param 2), but what this other program does to your screen is up to this process. Programs meant to be executed silently (should) accept arguments like --headless or /nogui, or (should) provide a suitable IPC (e.g. COM) interface. So how to start other programs 'in the background' can't be answered in a 'one strategy for all' way. AFAIK, the players offer COM/OCX interfaces, and using these certainly beats Sendkeys voodoo. So google for "iTunes.Application vbscript" or "Wmplayer.OCX." to get some hints about how to use these COM objects.
Instead of using the Shell Run method you could try the Create method of the WMI Win32_Process provider.
The example on this MSDN page creates a configuration object to set the process option ShowWindow to SW_NORMAL (i.e. 1) for a GUI executable - NOTEPAD.EXE.
On this page it looks like SW_HIDE (with a value of 0) is also an option.