I am thoroughly enjoying Mefilly's Megatron in To Build a Future. In it he is sane, calculating, and just everything I want in a sexy despot. It is post DOTM using the Novel ending in which Megatron and the 'Cons are now rebuilding Cybertron. It has elements from our co-authored story Patronus in it, but that does not need to be read to follow and enjoy.

ETA
I've thoroughly been enjoying the world/culture building in Razordragonfly's Five Million Years I feel like it has a very strong beginning and fascinating insights on Decepticon and Autobot culture from a Decepticon POV (Skywarp/TC G1)