A simple text file with the lines
Code:
@ECHO OFF
"C:\path\to\calibre\calibre.exe" --start-in-tray
should work fine. Make sure the tray icon is enabled in the calibre preferences for to actually start in the tray.
Rename the file filename.bat and do whatever you want with it.
Just a side note, depending on what version of windows you run, you may prefer to run a scheduled task to start calibre instead of a batch file in the startup folder.