>A bit of a pain that there's no universal one for all languages, but I guess that would be just too convenient...

Nix and GNU Guix are capable of filling this role. Not only can they do the things that the typical system package managers (dpkg, yum) lack, but they also do many things that language-specific package managers lack. Transactional upgrades, rollbacks, unprivileged package installation, gracefully handling multiple versions of the same software, system-wide deduplication, full system configuration (if you want to use their associated distro), etc.

I have read several Nix + Haskell success stories on various blogs, so I would say it's worth checking out. Nix and Guix are the future of package management.