A while back this tip was posted in the Forum. However the code is slightly wrong but the general idea is very good.
Here is my spin on it.
Contents of /layouts/shortcodes/comment.html
{{ with .Get 0 }}{{ .Inner }}{{ end }}
And in your markdown files use it like so:
{{% comment %}}Internal comment{{% /comment %}}
OR
{{< comment >}}Internal comment{{< /comment >}}
This shortcode basically looks for a parameter from its input and it will render .Inner only if that parameter exists.
Simply not providing that parameter will hide everything within the shortcode input from the HTML output.
Also note my use of the with function. This ensures that no errors are caused by the missing parameter.