If your using XP I can do this fairly easily.
As a test copy this script into the edit window here FBSL Studio
Make sure FBSL.exe is selected then download the exe. onto your machine.
Double click to run and it should fade your TaskBar. run it again to disable.
#dlldeclare user32.FindWindow,user32.SetLayeredWindowAttributes,user32.GetWindowLong _
Const LWA_ALPHA = &H2
Const GWL_EXSTYLE = (-20)
Const WS_EX_LAYERED = &H80000
hTaskBar = FindWindow("Shell_TrayWnd","")
Ret = GetWindowLong(hTaskBar, GWL_EXSTYLE)
SetWindowLong(hTaskBar,GWL_EXSTYLE,Ret + WS_EX_LAYERED)
If it works ok for you and anyone else who wants to test it (WinXP), I'll go ahead and create your application for you.