Use Layers Effectively

Although only 20 layers are available, Blender's layering system is very versatile and used for a variety of purposes. Objects can live on more than one layer, lights can be made to only illuminate the layers they're on, and you can use layers to animate the visibility of objects in your scene. As such, keeping some form of organization in mind is in your best interest.

One thing I like to do is place all my models on the top row of layers (layers 1–10) and all other objects, such as lights, cameras, and armatures, on the bottom row (layers 11–20).

Also keep high-priority objects, such as characters and animated things, on the left-most layers, while keeping static objects like backgrounds on the right-most layers.

Specifically for character animation, when I put my character in one layer, I place his rig in the layer directly below it. I like to stick to this little convention, which is certainly a help for me when I want to quickly make sense of a .blend file that I haven't opened in a long time.

Of course, this organizational style may not work for you, but you should definitely make it a point to create some conventions that you can remember and reuse.

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