It comes down to a choice between Blue and Green for me, as Red is out of the question since it kills the Geth, and my Shepard operates on a strict 'Say No to Genocide' policy. While Blue certainly offers the most definitive positive ending, what with the Reapers securing galactic peace and prosperity and offering huge scientific advancement, the possibilities that Green entails are too enticing to pass up. There is so much potential in the radical change presented there - how have the rules of mortality changed? Can you 'interface' with others, or your environment? Can you augment yourself? To what extent are you immediately changed by these events? Story-wise, it opens up whole avenues of possibilities, with different people and races coming to terms with their new situation and discovering what they can do, and that's too good to pass up.
Which is why it frustrates me to NO END that ALL the info you get on that is 'It's synthesis - organic + synthetic, Woo-ooh-ooh'. (Grumbles to self and walks away)
Amusingly appropriate Captcha: I want control