A gift certificate for a diploma framing. Look up her professional organization and if the "student" level membership is in your price range offer to pay for her joining or renewal (as a bonus these often come with an "insider" mag. subscription). A nice laptop bag in high quality nylon or leather (you can get great deals on these). Depending on employment situation, a set of small giftcards for things she enjoys but may not have cash for while on the job hunt (coffee, movies, Yankee candle, etc.). A massage gift certificate, or a mani-pedi. A gift card at a "professionalwear" type retailer to help get clothes together for the job hunt, new job, etc.
Other than that, you may actually want to skew in the direction of a gift for HER rather than a gift for a new Ph.D. Buying something to remind her to take care of herself may be the best gift (if she likes to workout, a certificate to a gym or yoga studio that focuses on wellness, gift card to her favorite workout clothing store, gift card to her favorite juice bar or healthfood store, spa, etc.)
