How to organize GameObjects in a Scene?

Obviously there are a Scene hierarchy, but the problem is that the scene hierarchy was not meant for organizing GameObjects because parent GameObjects affect the transformation of their children.

For example what can one do to select all the decoration GameObjects? Some might be children of non-decoration GameObjects and buried very deep in the scene hierarchy while others might be root GameObjects.

One solution could be to add a Tag, but since Unity restrict you to only one tag per GameObject, that makes the usage of tags pointless as I have different overlapping categories.

Another solution would be to name objects but that is very error prone as a typing mistake will loose my GameObject. Also the team need to memorize possible tokens in the name which allow even more room for human errors.

Another solution would be to add an identifying Component, similar to how tags work in most other applications. But will there be a penalty in build time/runtime in a large project because of the additional Scripts (Components)?

Any other ideas how I can organize my Scene so that I can easily select a logical group of GameObjects from different unrelated parents?

I would really love to see something like Cryengines layers system in unity, where you can put objects to separate layers, those are not objects in the scene and doesnt change children objects per object visibility when turned invisible, doesnt change tranform etc

What I do now, is having empty objects at scene 0 and use them to store objects, trying to not ever touch it. Works kind of okay for smaller project, imo not useable for anything bigger though.

@fildax Yes, that is basically what I was also doing so far. However, I have a much larger project now and would like to keep things organized. What you described in the Cryengine is exactly what I am looking for. I also know there are “Asset Labels” which would have worked too, but they are not available in the Unity Scene hierarchy and you can only search for them in the Project view. Don’t know if there are a way to write a special editor plugin or hack to make them available in the Scene too?