There are many ways to express gratitude for a graduation card. The best message is one that is personal and comes from the heart. A quick example would be: Thank you for the generous gift. It meant so much to me.
A good message for a graduation thank you note will vary on what type of gift has been received and who gifted it. If it was a cash gift, it would be nice to mention the generous check. If it was a specific gift such as a book or camera, it is good to mention the specific gift. Try to be as personal as possible when writing thank you notes for graduation gifts.