As far as Johns' best book or idea?
I would say JSA and Green Lantern.
My favorite things from him are 52 and his Green Lantern return through the end of Blackest Night. I liked Brightest Day at the beginning but I thought the ending was a dud. Well, actually, I did still like the post-Blackest Night GL titles, just not the Brightest Day weekly, so GL until the start of the New 52.
There's a ton of stuff I haven't read by him though.
Green Lantern Rebirth and pretty much his entire GL run. He returned Hal Jordan to main DC after he was very disrespectfully turned into a villain years prior. For me it is a near perfect retcon.