You can use AutoHotKey (which also has many other uses):
http://www.autohotkey.com/ For the script, just create a text file called startprogram.ahk with the following (this one starts Calculator):
SetTitleMatchMode 2
SetTitleMatchMode Fast
RunProgOnTop:
Run %windir%\system32\calc.exe, , , myopvar ;myopvar=variable to store the process id
WinWait ahk_pid %myopvar%
WinSet, AlwaysOnTop, On, ahk_pid %myopvar%
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