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Personally, I always like to use containers when possible. Keep in mind that unlike virts, containers have very minimal overhead. So there really is no practical cost to using them, and they provide better (though not perfect) security and some amount of sandboxing for every application.
Containers mean that you never have to worry about whether your VM is running the right versions of certain libraries. You never have to be afraid of breaking your setup by running a software update. They're simpler, more robust and more reliable. There are almost no practical arguments against using them.
And if you're running multiple services the advantages only multiply because now you no longer have to worry about running a bespoke environment for each service just to avoid conflicts.
Copying a response I wrote on another comment -
Thanks for this - the one advantage I'm noticing is that to update the services I'm running, I have to rebuild the container. I can't really just update from the UI if an update is available. I can do it, it is just somewhat of a nuisance.
How often are there issues with dependencies? Is that a problem with a lot of software these days?
Ok but containers generally have a lot less dependencies. If you are making your own images, then you know exactly how to rebuild them. In the event something happens, it makes it much easier to get up and running again and also remember what you did to get the service running. The only other thing that would be better is Nix.
If you use an image that someone is maintaining, this makes it even easier and there are services out there that will keep your containers up to date when a new image is available. You can also just automate your image builds to run nightly and keep it up to date.
There's no good answer to that because it depends entirely on what you're running. In a magical world where every open source project always uses the latest versions of everything while also maintaining extensive backwards compatibility, it would never be a problem. And I would finally get my unicorn and rainbows would cure cancer.
In practice, containers provide a layer of insurance that it just makes no sense to go without.