Once someone has a Ph.D. she will probably be going into the workforce where she can use her degree. A frame for her diploma is a perfect gift so she can proudly display it in her office or wherever she works. This lets everyone know her qualifications immediately and reminds her of all the hard work she put in to get where she is now.
After years of hard work and dedication in school, a vacation is well deserved. Get the Ph.D. graduate tickets to go somewhere relaxing for a week before he begins job hunting or begins the job he may already have found. Some resorts have all-inclusive packages so he won't have to worry about any fees, just relaxing and enjoying his time out of school.
Give your graduate a smart phone. Since he is out of school and will be joining the workforce at an advanced level due to his qualifications, he will need something to help keep him organized. Get him a phone that allows him to read emails, open and create documents, keep track of his calendar and anything else he may need for his profession. This phone will help him stay on track and always be in communication with people.
Since getting a Ph.D. requires years of schooling, it may also mean going into years of student-loan debit. One gift you can give her that will really help her out as she first begins her career is to help her pay the bills on a few of those loans. You can offer to pay for the first few months or give her "coupons" that she can redeem if she's ever in a jam and needs you to pay one. This gift is monetary but it gives her peace of mind.