The second post of this thread:
http://www.subsim.com/radioroom/showthread.php?t=173121
Has a very good and up to date list of mods, and they are installed in a good order. You see, when using JSGME, the order in which you install many mods is very important. If you follow this list though, you will be fine. Also, keep in mind that you don't have to have many of the mods in this list, what you install and what you don't is really all up to personal taste. Good luck