Basically I'm working on a tiered system. Files/dirs are categorized by size (<10MB, <25GB, >25GB) , and by sensitivity (public, confidential, secure. And importance is usually proportional to security). I have fortunately found that security is usually inverse to size. Github/lab anything which makes sense. Confidential small stuff (sans keys) is just stored in gmail/drive. Big, boring stuff (music, ebooks) is just kept on external hard drives.

Secure, ultra-important stuff, I don't really have a system for.

The system I'm leaning towards is just encrypt archives and store the key/password securely, and store it like you would any boring data, with a local NAS and a cloud backup service of some sort, or just stored on drives offsite.