Create an interesting format for your portfolio that will make your application stand out among other graduate portfolios. Don't just think about the material inside your portfolio, make the whole package stand out. However, don't make it too complicated or cumbersome. The admissions board should be able to access the work in your portfolio easily.
Tailor your portfolio to the kind of design work you want to do. At the undergraduate level, experiment in different disciplines, but graduate programs will expect you to specialize in a specific area. Carefully consider how the pieces in your portfolio reflect the kind of work you want to do in graduate school.
Limit the number of works you put in your portfolio. Check the admissions requirements to see if there's a required number of works. If not, try to include six to 10 of your best pieces. Show off some of your professional works, if you have any.
Project the images in your portfolio on a screen. Many admissions board will ask for digital submissions and review them by cycling through projected images. Preview them yourself to ensure that works still hold up on a large scale.
Create a website. Many graduate programs want to see a practical application of your design skills. Since more and more design work is being done for websites, you should consider setting up a model site that represents your best work. Provide the website as an online location for your portfolio. Don't forget to create an interesting logo and title page for your website.