In you PL/SQL Developer shortcut in the start menu, right mouse click and select properties. In the 'target' box you will find a command like: (double quotes included)
"C:\Program Files\plsql developer 7.1\PlSqlDev.exe"
If you want to add command line parameters, just put them after the command above, eg.
"C:\Program Files\plsql developer 7.1\PlSqlDev.exe" nosplash NoQueryHint desktop=my_desktop