Witchipedia

As with most things, it depends on context. In some cases, they are used to honor the Goddess of the Hunt, Artemis, Diana, similar. I think more common they represent the Horned God, often a God who dies and is reborn, so it may feature in rites for the dead and ancestors. I have seen a dance using antlers in this context. Deer hunting is popular in my area and I know at least one group of men who are hunters and honor the actual spirit of the deer and gather at the start of hunting season to honor the spirit and give thanks for the food it will provide and ensure the success of the hunt, a skull and horns are used in that ceremony, though I have not personally witnessed it and only happened to learn about it when I showed up to hang out with the wife as her husband was packing to go away for the weekend. I believe the stag/buck also features in men's mysteries, as a symbol of male virility and so might also be involved in manhood ceremonies and such.

I personally keep a deer skull (without horns) on my nature altar to represent the wild fauna part of nature. As a farmer and wildcrafter, I do a lot of work with my immediate natural surroundings. To me, the deer represents the critters that are going to come in and eat my garden so I relate to it from that angle.

Keep in mind though that outside of these contexts, the stag skull and antlers could mean something else entirely. It is a popular symbol in both spiritual and mundane contexts.