Here are a few of the wikis and guides I check out when I am stuck or questioning. Please add your own resources!
http://www.stowiki.org/Main_Page This is a good guide, but they have struggled to keep up with some of the more recent changes. Generally speaking, a good mission outline guide, and a great place to figure out where to go next when you are lost.
http://forums.startrekonline.com/showthread.php?t=60742 A nice FAQ for beginning (and even some veteran) players