Any Lightning equipped dock will charge and hold the Pencil when you use the included adapter, as already mentioned.
Or, Moxiware has a couple of really nice custom designed Pencil docks.
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They also do a magnetic sleeve for the Pencil so that you can attach it directly to the iPad, though I'm not so keen on the bump it adds to the Pencils nice clean lines.
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Or there's the Quarter from SteelConnect which slots into the Lightning port and you can slide the Pencil in there to stow it away.
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Here's my (very much less than elegant solution.)
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