If you want to simply reference Grapher in the body of the paper, you could use "GrapherTM from Golden Software, LLC (www.goldensoftware.com)" or "GrapherTM (Golden Software, LLC)". Grapher is trademarked, and so it has a TM after it.
If you want to reference Grapher at the end in a bibliography or reference list, our information is:
Golden Software, LLC.
PO Box 281
Golden, CO 80402-0281 USA