A combo of both. I group all my media apps like Sonarr, Radarr, SABnzbd, etc together in one compose since I consider each of them to be a part of the same “machine”, but most of my apps have their own compose.

I have an HP DL380 Gen8 and then a PC I bought from the local university and use as a server.

My DL380 runs ESXi. My PC runs Ubuntu on bare metal.

All of my apps are either fully VM-based (Home Assistant OS) or run in containers. Containers are far easier to build, upgrade, and migrate, and also make file management a lot easier.

I use Docker Compose. No Swarm or Kubernetes at this point.

Hopefully this is at least a good start! Let me know if you have any questions.