Well, nearly all of the best non-AO stuff has been mentioned (of which I'll second Chaos;Head, Steins;Gate, 999, Virtue's Last Reward, Corpse Party), I'll close that category with Planetarian - Reverie of a little Planet. And recommend a few less high profile non-AO titles, such as Higanbana no saku yoru, and Rose Guns Days. Also hear decent things about Rewrite.
The excellent Cross+Channel comes with an option for all ages install as well, but otherwise I'm out of titles which aren't AO-rated. Mostly AO content is merely a bother/bonus depending on taste, but in a few (Saya no Uta, Swan Song) it's an integral part of the plot.