It’s not strictly system neutral, but the Apocalypse World MC’s guide teaches a really neat style of GMing a sandbox campaign with almost entirely improv. I’ve explained it a bit in one of my GM Tech articles (GM Tech: How to be an MC) and I always think it’s worth a read.
On a similar vein, I’m also a fan of Microscope. It’s a sort-of-RPG system where a group of players work together to build a timeline and flesh out the history of a fictional world. It can be of great help when making a homebrew setting, and last time I used it all the players in the subsequent campaign independently gave their characters some sort of tie-in to important events in the recent past, which was really cool and made for an interesting story.