Go into your windows start menu and find the section Programs/Startup . You should find that Limewire has listed itself in this section.
Just right click and delete the Limewire reference there and Limewire will then only start when you want it to.
Don't forget that you will have to connect manually (File/connect) otherwise you will get no listing of songs or whatever you are searching for.
Very tricky this.. it knows how to put itself on the start menu but when you want to remove it you've got to do it manually.