Sorry for doubleposting, but I found a solution myself and I thought I let people know who might be searching for the same.
(I am on Windows 7 Home Premium RTM, things may be different for other Windows versions)
The solution to my problem above was, launch C:\Windows\WindowsMobile\wmdc.exe on startup.
Make a new shortcut, enter C:\Windows\WindowsMobile\wmdc.exe as shortcute, name it anything you like, and move it to the Startup folder under All Programs in your startmenu.
wmdc.exe is the Windows Mobile Device Center, which will start completely hidden and just sit there until you connect your phone and will take care of the automatic syncing.