I built a JSON templating system[0] (based on Handlebars) that is project based. Basically, you create new JSON files for each project and the system generates a CFN template that contains everything that project needs (EC2 instances, RDS instances, security groups, etc.) It's still a work in progress but I'm using it in production in my day job and I'm pretty happy with how it works. More help is always accepted. :)

[0] https://github.com/rnhurt/CFNBuilder